EP2114429A2 - Compositions and methods to prevent cancer with cupredoxins - Google Patents

Compositions and methods to prevent cancer with cupredoxins

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Publication number
EP2114429A2
EP2114429A2 EP08743447A EP08743447A EP2114429A2 EP 2114429 A2 EP2114429 A2 EP 2114429A2 EP 08743447 A EP08743447 A EP 08743447A EP 08743447 A EP08743447 A EP 08743447A EP 2114429 A2 EP2114429 A2 EP 2114429A2
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European Patent Office
Prior art keywords
cupredoxin
giy
ala
cancer
cells
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
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EP08743447A
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German (de)
French (fr)
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EP2114429A4 (en
Inventor
Tapas Das Gupta
Ananda Chakrabarty
Craig Beattie
Tohru Yamada
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University of Illinois
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University of Illinois
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Publication of EP2114429A2 publication Critical patent/EP2114429A2/en
Publication of EP2114429A4 publication Critical patent/EP2114429A4/en
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    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • A—HUMAN NECESSITIES
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    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/164—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
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    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/54—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
    • A61K47/549—Sugars, nucleosides, nucleotides or nucleic acids
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    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/62—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being a protein, peptide or polyamino acid
    • A61K47/64—Drug-peptide, drug-protein or drug-polyamino acid conjugates, i.e. the modifying agent being a peptide, protein or polyamino acid which is covalently bonded or complexed to a therapeutically active agent
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/0002—General or multifunctional contrast agents, e.g. chelated agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/04—X-ray contrast preparations
    • A—HUMAN NECESSITIES
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    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/06—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations
    • A61K49/08—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations characterised by the carrier
    • A61K49/085—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations characterised by the carrier conjugated systems
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K49/00—Preparations for testing in vivo
    • A61K49/06—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations
    • A61K49/08—Nuclear magnetic resonance [NMR] contrast preparations; Magnetic resonance imaging [MRI] contrast preparations characterised by the carrier
    • A61K49/10—Organic compounds
    • A61K49/14—Peptides, e.g. proteins
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61M—DEVICES FOR INTRODUCING MEDIA INTO, OR ONTO, THE BODY; DEVICES FOR TRANSDUCING BODY MEDIA OR FOR TAKING MEDIA FROM THE BODY; DEVICES FOR PRODUCING OR ENDING SLEEP OR STUPOR
    • A61M5/00—Devices for bringing media into the body in a subcutaneous, intra-vascular or intramuscular way; Accessories therefor, e.g. filling or cleaning devices, arm-rests
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
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    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/21—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Pseudomonadaceae (F)
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    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/22—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Neisseriaceae (F)
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    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/225—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Alcaligenes (G)
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    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/235—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Bordetella (G)
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    • C07—ORGANIC CHEMISTRY
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    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/28—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Vibrionaceae (F)
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    • C07—ORGANIC CHEMISTRY
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    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/32—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Bacillus (G)
    • C—CHEMISTRY; METALLURGY
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    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/02—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms
    • C12Q1/025—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/02—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving viable microorganisms
    • C12Q1/04—Determining presence or kind of microorganism; Use of selective media for testing antibiotics or bacteriocides; Compositions containing a chemical indicator therefor
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61K38/00—Medicinal preparations containing peptides
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y5/00—Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery

Definitions

  • the present invention relates to compositions comprising variants, derivatives and structural equivalents of cupredoxins that inhibit the development of premalignant lesions in mammalian ceils, tissues and animals.
  • the invention also relates to the use of cupredoxins. and variants, derivatives and structurally equivalents of cupredoxins, as chemopre ⁇ entive agents in mammals to inhibit the development of premalignant lesions, and ultimately cancer.
  • Cancer chemoprevention is the use of natural, synthetic or biologic chemical agents to reverse, suppress, or prevent carcinogenic progression to invasive cancer. Recent clinical trials in preventing cancer in high-risk populations suggest that chemopreventive therapy is a realistic treatment for high-risk patients.
  • Chemopreventive therapy is based on the concepts of multifocal field carcinogenesis and multistep carcinogenesis. In field carcinogenesis, generalized carcinogen exposure throughout the tissue field results in diffuse epithelial injury in tissue and clonal proliferation of the mutated cells. These genetic mutations throughout the field increase the likelihood that one or more premalignant or malignant lesions may develop in the field. Multistep carcinogenesis in the stepwise accumulation of these genetic and phenotypic alterations.
  • Arresting one or more steps in the multistep cancinogenesis may impede or prevent the development of cancer. See generally Tsao ct ah, CA Cancer J Clin 54: 150-180 (2004).
  • Azurin, and other cupredoxins. are cytotoxic specifically towards cancer cells. Azurin induces apoptosis in J774 lung cancer cells. Yamada et ah, PNAS 99(22): 14098-14103 (2002).
  • azurin localizes in the cytosol and nuclear fractions, and forms a complex with tumor suppressor protein p53, thereby stabilizing it and enhancing its intracellular level. Id.
  • azurin-mediated apoptosis is not limited to J774 cells.
  • Azurin can also enter cancer cells such as human melanoma UISO- MeI -2 or human breast cancer MCF-7 cells.
  • Yamada ct ai Infect ⁇ nimun. 70:7054-7062 (2002); Punj et ah, Oncogene. 23:2367-2378 (2004).
  • azurin allowed the elevation of the intracellular p53 levels, leading to enhanced Bax formation and induction of apoptosis in such cells.
  • intraperitoneal injection of azurin in nude mice harboring xenografted Mel-2 or MCF-7 human cancers led to statistically significant regression of such cancers. Id.
  • the mouse mammary gland organ culture (MMOC) assay may be used to evaluate the inhibitory effects of potential chemopreventive agents on both hormone-induced structural differentiation of mammary glands and on the development of DMBA-induced preneoplastic hyperplastic alveolar nodule-like lesions in the gland.
  • mice exhibit a distinct preneoplastic stage prior to cancer formation in MMOC.
  • Such preneoplastic lesions in C3H mice are induced by murine mammary tumor virus or in BALB'c mice by DMBA.
  • MAL mammary alveolar lesions
  • DMBA-induced mammary lesion formation in MMOC can be inhibited by a variety of classes of chemopreventive agents such as retinoids.
  • chemopreventive agents such as retinoids.
  • These agents include chemopreventive agents derived from the natural products such as brassinin and resveretrol, thiols, antioxidants, inhibitors of ornithine decarboxylase such as OFMO and deguelin, inhibitors of prostaglandin synthesis, Ca regulators, etc., Jang et al., Science 275:218-220 (1997); Mehta, Eur. J. Cancer 36:1275-1282 (2000); Metha et al., J. Natl. Cancer Inst. 89:212-219 (1997).
  • These studies clearly demonstrate that this organ culture system offers a unique model to determine the effectiveness of compounds against mammary carcinogenesis. The results can be expected to closely correlate to the inhibition obtained by in vivo administration of such compounds
  • the MMOC may also be induced to form mammary ductal lesions (MDL).
  • MDL mammary ductal lesions
  • the MDL can be induced if estrogen and progesterone instead of aldosterone and hydrocortisone are included in the medium
  • the alveolar structures in the presence of ovarian steroids are very small but the intraductal lesions are observed in histupathol ⁇ gica! sections. Mehta ei al, J Natl. Cancer Inst. 93: 1 103-1 106 (2001).
  • the antiestrogens which selectively work on ovarian hormone dependent ER+ breast cancers such as tamoxifen, inhibited MDL formation and not MAL.
  • this modified culture model in addition to conventional MAL induction protocol now can be used to evaluate effects of chemopreventive agents on both MAL and MOL.
  • chemopreventive agent that inhibit the development of premalignant lesions.
  • a chemopreventive agent should be able to either prevent the initial development of premalignant lesions, induce cell death m premalignant lesions that form, and/or prevent the development of premalignant lesions into malignant lesions.
  • Such chemopreventive agents would have great utility in treating, in particular, patients who are at a high risk of developing cancer, due to either the presence of high-risk features, the presence of pre-malignant lesions, or the previous of cancer or premalignant lesions.
  • a protein transduction domain The entry of a protein into a mammalian cell is often dictated by a small segment of the protein, which is commonly referred to as a "protein transduction domain" or PTD.
  • This segment can be used as a signal attached to a foreign protein to facilitate transport of such a protein into a mammalian cell.
  • amphipathic peptides are used to facilitate uptake of DNA-cleaving metalloporphyrins as potential antitumor drugs in human fibroblasts HS68 or murine lymphocytic leukemia L1210 cells (Chaloin, L. et al. Bioconjugate Chem. 12:691-700, (2001)).
  • Peptides called cell-penetrating peptides, such as penetratin, transportan, Tat (amino acids 47-57 or 48-60) and the model amphipathic peptide MAP, have been used as delivery vehicles for transporting pharmacologically important substances, such as antisense oligonuclotides, proteins and peptides (Hallbrink, M. et al. Biochim. Biophys. Acta 1515:101-109 (2001); Lindgren. M., et al Trends Pharmacol. Sci. 21 :99-103 (2000)).
  • Such peptides are internalized by many types of cells in culture, such as human HS6S or murine N ⁇ H-3T3 fibroblasts, at either 37 0 C or 4 0 C.
  • the lack of effect of the temperature shift suggests a penetration mechanism different from that of classical endocytosis (Morris. M. C. et al Nature Biotechnol. 19:1173- 1176 (2001)), which requires chiral receptor proteins.
  • This short peptide domain of HIV-I Tat has been shown to mediate cell internalization of large molecules or particles, including magnetic nanopartieles, phage vectors, liposomes and plasmid DNA. Unlike the other cell-penetrating peptides discussed above, internalization of cargo proteins by full length Tat or its 11 amino acid transduction domain is significantly impaired at 4 0 C (Uu. Y. et al Nat. Med. 6: 1380-1387 (2000). Suzuki, T. et al J. Biol. Chem. 277:2437-2443 (2002)) and requires interactions with receptors such as the heparan sulfate chains of the cell membrane heparan sulfate proteoglycans.
  • PTDs Most of the PTDs identified to date have been derived from viral and mammalian sources. Other sources of PTDs would be desirable for the design of various experimental sequences, and for animal and human therapies and prophylactic procedures.
  • One alternative source of PTDs is bacterial cells. Although bacterial proteins such as cholera toxin are known to enter mammalian cell cytosol (Sofer, A. and Futerman, A.H. J. Biol. Chem.
  • the present invention relates to compositions comprising peptides that may be variants, derivatives and structural equivalents of cupredoxins that inhibit the development of premalignant lesions in mammalian cells, tissues and animals.
  • these compositions may comprise azurin from Pseudomonas aeruginosa, the 50-77 residue region of azurin (p28) SEQ ID NO: 2, and the 50-67 residue region of a/urin (ptS) SEQ ID NO: 25
  • the present invention further relates to compositions that may comprise cupredoxin(s), and/or variants, derivatives or structural equivalents of cupredoxins, that retain the ability to inhibit the development of premalignant lesions in mammalian cells, tissues or animals.
  • compositions may be isolated peptides or pharmaceutical compositions, among others.
  • the compositions of the invention may be used in methods to prevent the development of cancer in mammalian patients.
  • One aspect of the invention are isolated peptides that may be a variant, derivative or structural equivalent of a cupredoxin; and may inhibit the development of premalignant lesions in mammalian tissue.
  • the cupredoxin may be azurin, pseudoazurin, plastocyanin, ruslicyanin. Laz, auracyanin, stellacyanin and cucumber basic protein, and specifically may be azurin.
  • the cupredoxin may be from an organism such as Pseudomonas aeruginosa.
  • the peptide may be part of SEQ ID NOS: 1, 3-19, or has at least 80% amino acid sequence identity to SEQ ID NOS: 1, 3-19.
  • the isolated peptide may be a truncation of a cupredoxin.
  • the isolated peptide may be more than about 10 residues and not more than about 100 residues.
  • the isolated peptide may comprise, or alternatively consist of, Pseudomonas aeruginosa azurin residues 50-77 SEQ ID NO: 2, Pseudomonas aeruginosa azurin residues 50-67 SEQ ID NO: 25, Pseudomonas aeruginosa azurin residues 36-88 SEQ ID NO. 26, or SEQ ID NOS: 20-24.
  • cupredoxins may comprise at least one, or two, cupredoxins or isolated peptides of the invention in a pharmaceutically acceptable carrier.
  • the pharmaceutical composition maybe formulated for intravenous administration.
  • the cupredoxin in the pharmaceutical composition maybe from an organism such as Pseudomonas aeruginosa, Ulva pertussis, Alcaligenes faecalis, Achromobacter xylosoxidan, Bordetella bronchiseptica, Methylomonas sp., Neisseria meningitidis, Neisseria gonorrhea, Pseudomonas fluorescens, Pseudomonas chlororaphis, Xyiella fastidiosa and Vibrio par ahaernolyticus, and specifically may be from Pseudomonas aeruginosa.
  • the cupredoxin may be SEQ ID NOS: 1 , 3-19
  • Another aspect of the invention is a method to treat a mammalian patient by administering to the patient a therapeutically effective amount of the pharmaceutical composition of the invention.
  • the patient may be human, and may be at a higher risk to develop cancer than the general population.
  • the cancer may be melanoma, breast, pancreas, glioblastoma, astrocytoma, lung, colorectal, neck and head, bladder, prostate, skin, or eerviea! cancer.
  • the patient may have at least one high risk feature, premalignarit lesions or have been cured of cancer or premalignant lesions.
  • the pharmaceutical composition may be administered by intravenous injection, intramuscular injection, subcutaneous injection, inhalation, topical administration, transdermal patch, suppository, ⁇ itreous injection or oral, and specifically may be administered by intravenous injection.
  • the pharmaceutical composition may be coadministered with at least one other chemopreventive drug, and specifically at about the same time as another chemopreventive drug.
  • kits comprising the pharmaceutical composition of the invention in a vial.
  • the kit may be designed for intravenous administration.
  • Another aspect of the invention is a method to study the development of cancer comprising contacting mammalian cells with a cupredoxin or peptide of the invention and measuring the development of premalignant and malignant cells.
  • the cells may be human and/or mammary cells.
  • the cells are induced to develop premalignant lesions.
  • Another aspect of the invention is an expression vector, which encodes a peptide of the invention.
  • Another aspect of the invention is a complex comprising a cargo compound and an amino acid sequence, where the amino acid sequence has at least about 90% sequence identity with a cupredoxin, or a fragment thereof, the amino acid sequence, or fragment thereof, is linked to the cargo compound, and the amino acid sequence facilitates entry of the cargo compound into a mammalian cancer cell.
  • the amino acid sequence of this complex has at least about 90% amino acid sequence identity to less than a full length wild-type cupredoxin or H.8 outer membrane protein
  • the cargo compound is protein, lipoprotein, polypeptide, peptide, polysaccharide, nucleic acid, dye, micropatiiele, iia ⁇ oparticle, toxin and drug
  • the cargo is a protein or polypeptide which is linked amino acid sequence to form a fusion protein.
  • the cargo compound is a toxin, more particularly, the Pseudomonas aeruginosa exotoxin A.
  • the cargo is a detectable substance, more specifically one detectable by fluorimetry. microscopy, X-ray CT, MRI or ultrasound.
  • the invention also encompasses the complex in a pharmaceutically suitable carrier.
  • Another aspect of the present invention is directed to a method for delivering a cargo compound into a cell.
  • this method comprises contacting a cell or cells with the above complex.
  • the ceil or cells originate from a patient suffering from cancer, and are reintroduced into the patient.
  • the cells is a cancer cell, more specifically an osteosarcoma cell, lung carcinoma cell, colon carcinoma cell, lymphoma cell, leukemia cell, soft tissue sarcoma cell, breast carcinoma cell, liver carcinoma cell, bladder carcinoma cell or prostate carcinoma cell
  • the complex is administered to a patient in a therapeutically effective amount.
  • the complex is administered intravenously, topically, subcutaneous Iy, intramuscularly or into a tumor.
  • the complex is co-administered with another cancer treatment.
  • RNAi approaches, drug resistance, hematopoietic gene transfer, homologous recombination, ribozyme technology, antisense technology, tumor immunotherapy and tumor suppressors.translational research, cancer therapy, gene delivery systems (viral and non- viral), anti-gene therapy (antisense, siRNA & ribozymes), apoptosis; mechanisms and therapies , vaccine development, immunology and immunotherapy, and DNA synthesis and repair are used in the context of delivering DNA and/or RNA as cargo compounds in the complexes of the present invention.
  • the cargo compound is an antisense molecule.
  • the complex with a cargo that is a detectable substance is administered to a patient with cancer and the location of the cargo is detected.
  • the cargo compound is an X-ray contrast agent and is detected by X-ray CT
  • the cargo compound is a magnetic resonance imaging contrast agent and is detected by MRI
  • the cargo is an ultrasound contrast agent and is detectable by ultrasound
  • the a cell or cells are contacted with a complex with a detectable substance and the location of the cargo is detected.
  • kits that contains any of the above complexes.
  • the kit further comprises a pharmaceutically acceptable adjuvant or excipient.
  • the kit further comprises a vehicle for administration of the reagent.
  • SEQ ID NO: 1 Amino acid sequence of azurin from Pseudomonas aeruginosa (Ala GIu Cys Ser VaI Asp Be GJn GIy Asn Asp GIn Met GIn Phe Asn Thr Asn Ala He Tlir VaI Asp Lys Ser Cys Lys GIn Phe Thr VaI Asn Leu Ser His Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp Ser Arg VaI lie Ala His Thr Lys Leu He GIy Ser GIy GIu Lys Asp Ser VaI Thr Phe Asp VaI Ser Lys Leu Lys GIu GIy GIu GIn Tyr Met Phe Phe Cys Thr Phe Pro Thr
  • SEQ ED NO: 3 Amino acid sequence of plastocyanin from Phormidium laminosum (GIu Thr Phe Thr VaI Lys Met GIy Ala Asp Ser GIy Leu Leu Gin Phe GIu Pro Ala Asn VaI Thr VaI His Pro GIy Asp Thr VaI Lys Trp VaI Asn Asn Lys Leu Pro Pro His Asn He Leu Phe Asp Asp Lys GIn VaI Pro GIy Ala Ser Lys GIu Leu Ala Asp Lys Leu Ser His Ser GIn Leu Met Phe Ser Pro GIy GIu Ser Tyr GIu He Thr Phe Ser Ser Asp Phe Pro Ala GIy Thr Tyr Thr Tyr Tyr Cys Ala Pro His Arg GIy Ala GIy Met VaI GIy Lys He Thr VaI GIu GIy).
  • SEQ ID NO: 4 Amino acid sequence of rusticyanin from Thiobacillus ferrooxidans (GIy Thr Leu Asp Thr Thr Trp Lys GIu Ala Thr Leu Pro GIn VaI Lys Ala Met Leu GIu Lys Asp Thr GIy Lys VaI Ser GIy Asp Thr VaI Thr Tyr Ser GIy Lys Thr VaI His VaI VaI Ala Ala Ala VaI Leu Pro GIy Phe Pro Phe Pro Ser Phe GIu VaI His Asp Lys Lys Asn Pro Thr Leu GIu He Pro Ala GIy Ala Thr VaI Asp VaI Thr Phe He Asn Thr Asn Lys GIy Phe GIy His Ser Phe Asp lie Thr Lys Lys GIy Pro Pro Tyr Ala VaI Met Pro VaI He Asp Pro He VaI AIa GIy Thr GIy Phe Ser Pro VaI Pro Lys Asp GIy Lys Phe
  • SEQ ID NO: 7 Amino acid sequence of azurin from Achromobacter xylosoxidans ssp. denitrificans I (Ala GIn Cys GIu Ala Thr He GIu Ser Asn Asp Ala Met GIn Tyr Asn Leu Lys GIu Met VaI VaI Asp Lys Ser Cys Lys GIn Phe Thr VaI His Leu Lys His VaI GIy Lys Met Ala Lys VaI Ala Met GIy His Asn Trp VaI Leu Thr Lys GIu Ala Asp Lys GIn GIy VaI Ala Thr Asp GIy Met Asn AIa GIy Leu AIa GIn Asp Tyr VaI Lys Ala GIy Asp Thr Arg VaI He Ala His Thr Lys VaI He GIy GIy GIy GIu Ser Asp Ser VaI Thr Phe Asp VaI Ser Lys Leu Thr Pro GIy GIu Ala Tyr Ala Tyr
  • SEQ ID NO: 8 Amino acid sequence of azurin from Bordetella bronchiseptica (Ala GIu Cys Ser VaI Asp He Ala GIy Thr Asp GIn Met GIn Phe Asp Lys Lys Ala He GIu VaI Ser Lys Ser Cys Lys GIn Phe Thr VaI Asn Leu Lys His Thr GIy Lys Leu Pro Arg Asn VaI Met GIy His Asn Trp VaI Leu Thr Lys Thr AIa Asp Met GIn Ala VaI GIu Lys Asp GIy He Ala Ala GIy Leu Asp Asn GIn Tyr Leu Lys Ala GIy Asp Thr Arg VaI Leu AIa His Thr Lys VaI Leu GIy GIy GIy GIu Ser Asp Ser VaI Thr Phe Asp VaI Ala Lys Leu Ala AIa GIy Asp Tyr Thr Phe Phe Cys Ser Phe Pro a
  • SEQ ID NO: 10 Amino acid sequence of azurin from Neisseria meningitidis Z2491 (Cys Ser GIn GIu Pro Ala Ala Pro Ala Ala GIu Ala Thr Pro Ala Ala GIu Ala Pro Ala Ser GIu Ala Pro Ala Ala GIu Ala Ala Pro Ala Asp Ala Ala GIu Ala Pro Ala Ala GIy Asn Cys Ala Ala Thr VaI GIu Ser Asn Asp Asn Met GIn Phe Asn Thr Lys Asp He GIn Vai Ser Lys Ala Cys Lys GIu Phe Thr He Thr Leu Lys His Thr GIy Thr GIn Pro Lys Thr Ser Met GIy His Asn He VaI lie GIy Lys Thr GIu Asp Met Asp GIy He Phe Lys Asp GIy VaI GIy Ala Ala Asp Thr Asp Tyr VaI Lys Pro Asp Asp
  • SEQ ID ⁇ Q- 14 Amino acid sequence of stellacyanm from Cueumis saiivus (Met Gin Ser Thr VaI His He VaI GIy Asp 4sn Thr GSy Trp Ser Va! Pro Ser Ser Pro Asn Phe Tyr Ser GIn Tip Ala Ala GIy Lys Thr Phe Arg VaI GIy Asp Ser Leu GIn Phe Asn Phe Pro Ala Asn Ala His Asn VaI His GIu Met GIu Thr Lys GIn Ser Phe Asp Ala Cys Asn Phe VaI Asn Ser Asp Asn Asp VaI GIu Arg Thr Ser Pro Va!
  • SEQ ID NO: 15 Amino acid sequence of auraeyanin A from Chloroflexus auranttacus (Met Lys He Thr Leu Arg Met Met VaI Leu Ala VaI Leu Thr Ala Met Ala Met VaI Leu Ala Ala Cys GIy GIy GIy GIy Ser Ser GIy GIy Ser Thr GIy GIy GIy Ser GIy Ser GIy Pro VaI Thr He GIu He GIy Ser Lys GIy GIu GIu Leu Ala Phe Asp Lys Thr GIu Leu Thr VaI Ser Ala GIy GIn Thr VaI Thr He Arg Phe Lys Asn Asn Ser Ala VaI GIn GIn His Asn Trp He Leu VaI Lys GIy GIy GIu Ala GIu Ala Ala Asn He Ala Asn Ala GIy Leu Ser Ala GIy Pro Ala Ala Ala Asn Tyr Leu Pro
  • SEQ ID NO: 16 Amino acid sequence of auraeyanin B from Chloroflexus aurantiacus (Ala Ala Asn Ala Pro GIy GIy Ser Asn VaI VaI Asn GIu Thr Pro Ala GIn Thr VaI GIu VaI Arg AIa Ala Pro Asp Ala Leu Ala Phe Ala GIn Thr Ser Leu Ser Leu Pro Ala Asn Thr VaI VaI Arg Leu Asp Phe VaI Asn GIn Asn Asn Leu GIy VaI GIn His Asn Trp VaI Leu VaI Asn GIy GIy Asp Asp VaI Ala Ala Ala VaI Asn Thr Ala Ala GIn Asn Asn Ala Asp Ala Leu Phe VaI Pro Pro Pro Asp Thr Pro Asn Ala Leu Ala Trp Thr AIa Met Leu Asn Ala GIy GIu Ser GIy Ser VaI Thr Phe Arg Thr Pro Ala Pro
  • SEQ ID KO 17. Amino acid sequence of cucumber basic protein from Cucumis sativus (Ala VaI Tyr VaI VaI GIy Gl> Ser GIy GIy Trp Thr Phe Asn Thr GIu Ser Trp Pro Lys GIy Lys Arg Phe Arg Ala GIy Asp He Leu Leu Phe Asn Tyr Asn Pro Ser Met His Asn VaI VaI VaI Asn GIn GIy GIy Phe Ser Thr Cys Asn Thr Pro Ala GIy Ala L>s VaI Tyr Thr Ser GIy Arg Asp GIn lie Lys Leu Pro Lys GIy GIn Ser Tyr Phe He Cys Asn Phe Pro GIy His Cys GIn Ser GIy Met Lys He Ala VaI Asn AIa Leu).
  • SEQ ID NO: 18 Amino acid sequence of Laz from Neisseria gonorrhoeae F62 (Cys)
  • Chloroflcxus aurantiacus His Asn Trp VaI Leu VaI Asn GIy GIy Asp Asp VaI Ala Ala Ala VaI Asn Thr Ala Ala GIn Asn Asn Ala Asp Ala Leu Phe Va! Pro Pro Pro Asp).
  • SEQ ID NO: 21 Amino acid sequence of amino acids 51-77 of Ps eudomonas syringae azurin (Ser Lys Lys AIa Asp Ala Ser Ala He Thr Thr Asp GIy Met Ser VaI GIy He Asp Lys Asp Tyr VaI Lys Pro Asp Asp).
  • SEQ ID NO: 22 Amino acid sequence of amino acids 89-115 of Neisseria meningitidis Laz (He GIy Lys Thr GIu Asp Met Asp GIy He Phe Lys Asp GIy VaI GIy AIa AIa Asp Thr Asp Tyr VaI Lys Pro Asp Asp).
  • SEQ ID NO: 23 Amino acid sequence of amino acids 52-78 of Vibrio parahaemolyticus azurin (AIa Asp Thr Ala Asn He GIn Ala VaI GIy Thr Asp GIy Met Ser Ala GIy Ala Asp Asn Ser Tyr VaI Lys Pro Asp Asp).
  • SEQ ID NO: 24 Amino acid sequence of amino acids 51 -77 of BordeicHa br ⁇ nchiseptica azurin (Thr Lys Thr AIa Asp Met GIn Ala VaI GIu Lys Asp GIy He Ala Ala GIy Leu Asp Asn GIn Tyr Leu Lys Ala GIy Asp).
  • SEQ ID NO: 25 Amino acid sequence of pi 8, Pscudomonas aeruginosa azurin residues 50-67 (Leu Ser Thr Ala Ala Asp Met Gk GIy VaI VaI Thr Asp Gh Met Ala Ser Gl> ⁇ SEQ ID NO: 26.
  • Amino acid sequence of amino acids 36-88 of Pseudomonas aeruginosa azurin Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp Ser Arg VaI He Ala His Thr Lys Leu He GIy). SEQ ID NO: 27.
  • Amino acid sequence of amino acids 36 to 77 of Pseudomonas aeruginosa azurin Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp).
  • SEQ ID NO: 28 Amino acid sequence of amino acids 36 to 89 of Pseudomonas aeruginosa azurin (Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp Ser Arg VaI lie Ala His Thr Lys Leu He GIy Ser).
  • SEQ ID NO: 29 Amino acid sequence of amino acids 36 to 128 of Pseudomonas aeruginosa azurin (Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp Ser Arg VaI He Ala His Thr Lys Leu He GIy Ser GIy GIu Lys Asp Ser VaI Thr Phe Asp VaI Ser Lys Leu Lys GIu GIy GIu GIn Tyr Met Phe Phe Cys Thr Phe Pro GIy His Ser Ala Leu Met Lys GIy Thr Leu Thr Leu Lys).
  • SEQ ID NO: 30 Amino acid sequence of amino acids 53 to 70 of Pseudomonas aeruginosa azurin (Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys).
  • SEQ HD NO: 31 Amino acid sequence of amino acids 53 to 64 of Pseudomonas aeruginosa azurin (Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met).
  • Figure 1 depicts photographs of all of the glands evaluated for the efficacy of p28 and azu ⁇ n.
  • Figure IA shows a representative photograph of alveolar lesions in a DMBA-treated gland and its comparison with a gland that was treated with DMBA along with a chemopreventive agent.
  • Figures IB- IF show representative photographs of the effects of p28 on the development of aheolar lesions.
  • Figure 2 depicts a graph showing the efficacy of p28 against DMBA- induced mammary alveolar lesions.
  • Figure 3 depicts photographs of representative sections of ductal lesions and effect of p28.
  • Figure 4 depicts a graph showing the efficacy of p28 against DMBA- induced ductal lesions
  • Figure 5 Diagram showing the localization of the ⁇ -helix in wt-azurin as well as in the wt-azurin 50-77 protein transduction domain. Replacement of three amino acids in the azurin 50-77 domain by proline residues is indicated.
  • FIG. 6 (A), (B) and (C).
  • the gfp gene was introduced at the 3'-end of the gst gene (for GST- GFP) and the azu 50-77 fragment was then Iigated at the 3 ! -end of the gfp gene in frame to produce the GST-GFP-azu 50-77 fusion protein.
  • GST-GFP-azu 50-77 was purified as a single fusion protein from the cell lysates. Purified proteins were run on SDS-PAGE and detected by Coomassie Blue staining (6(B) and also by Western blotting using anti-azurin antibody (6(C)).
  • FIG. 7 (A), (B) and (C). Diagrams showing a kinetic study for the internalization of GST-Green Fluorescent Protein (GFP) and GST-GFP-azunn fusion proteins. Green fluorescence was assayed in J774 ceils treated with various concentrations of GST-GFP (10(a)) or GST-GFP-azu 50-77 (IG(B)) at 37°C for 1 hr. Ten thousand cells were analyzed by flow cytometry, (c) Time-dependence of internalization of GST-GFP-azu 50-77. J774 cells were incubated with 200 ⁇ g/tnl GST-GFP-azu 50-77 for indicated times at 37°C and analyzed by flow cytometry.
  • GFP GST-Green Fluorescent Protein
  • FIG. 8 (A), (B) and (C).
  • A Diagram showing the exotoxin A domain ⁇ I ⁇ (ammo acids 405-M3). as well as part of domain Ib (amino acids 381-404), fused to GSl (GST- PEDIII) as earlier described for the GST-GFP fusion. The azu 50-77 fragment was then ligated to the carboxyl end of GST-PEDIII (GST-PEDIII-azu 50-77), using PCR.
  • B The fusion proteins were purified by glutathione Sepharose 4B column gel filtration column chromatography and ran on SDS-PAGE for size determination.
  • C Diagram showing action of GST-PED ⁇ II-azu 50-77 fusion protein in UISO-Mel-2 cancer cells and in normal fibroblast (FBT) cells, as determined by PEDlII-mediated cytotoxicity.
  • Various concentrations, as indicated, of GST-PEDIII and GST-PEDIII-azu 50-77 were incubated with UISO-Mel-2 and FBT cells for 24 h, after which the cell viability was determined by MTT assay.
  • Figure 9 Diagram PEDHI-rnediated cytotoxicity of GST-PED Ill-rusticyanin fusion protein against UISO-Mel-2 cancer cells and FBT cells. Various concentrations, as indicated. of GST-PEDIII and GST-PEDIII-azu 50-77 were incubated with UISO-Mel-2 and FBT cells for 24 h, after which the cell viability was determined by MTT assay.
  • cell includes either the singular or the plural of the term, unless specifically described as a “single cell.”
  • polypeptide As used herein, the terms “polypeptide,” “peptide,” and “protein” are used interchangeably to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid. The terms also apply to naturally occurring amino acid polymers.
  • polypeptide “peptide,” and “protein” are also inclusive of modifications including, but not limited to. glycosylation, lipid attachment, sulfation, gamma- carboxylation of glutamic acid residues, hydroxylation and ADP-ribosylation. It will be appreciated thai polypeptides are not always entirely linear.
  • polypeptides may be branched as a result of ubiquitination and they may be circular (with or without branching), generally as a result of post-translation events, including natural processing event and events brought about by human manipulation which do not occur naturally.
  • Circular, branched and branched circular polypeptides may be synthesized by non-translation natural process and by entirely synthetic methods as well.
  • the term "pharmacologic activity” means the effect of a drug or other chemical on a biological system, The effect of chemical may be beneficial ⁇ therapeutic) or harmful (toxic).
  • the pure chemicals or mixtures maybe of natural origin (plant, animal, or mineral) or may be synthetic compounds.
  • premalignant means precancerous, or before abnormal cells divide without control.
  • lesion means an area of abnormal tissue.
  • pathological condition includes anatomic and physiological deviations from the normal that constitute an impairment of the normal state of the living animal or one of its parts, that interrupts or modifies the performance of the bodily functions, and is a response to various factors (as malnutrition, industrial hazards, or climate), to specific infective agents (as worms, parasitic protozoa, bacteria, or viruses), to inherent defects of the organism (as genetic anomalies), or to combinations of these factors.
  • condition includes anatomic and physiological deviations from the normal that constitute an impairment of the normal state of the living animal or one of its parts, that interrupts or modifies the performance of the bodily functions.
  • shuffering from includes presently exhibiting the symptoms of a pathological condition, having a pathological condition even without observable symptoms, in recovery from a pathological condition, or recovered from a pathological condition.
  • chemoprevention is the use of drugs, vitamins, or other agents to try to reduce the risk of, or delay the development or recurrence of, cancer.
  • treatment includes preventing, lowering, stopping, or reversing the progression or severity of the condition or symptoms associated with a condition being treated.
  • treatment includes medical, therapeutic, and/or prophylactic administration, as appropriate. Treatment may also include preventing or lessening the development of a condition, such as cancer.
  • inhibite cell growth means the slowing or ceasing of cell division and or cell expansion. This term also includes the inhibition of cell development or increases in cell death.
  • a “therapeutically effective amount” is an amount effective to prevent, lower, stop or reverse the development of, or to partially or totally alleviate the existing symptoms of a particular condition for which the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled m the art
  • the term “"substantially pure” refers to a factor in an amount of at least about 75%, by dry weight, of isolated fraction, or at least "75% substantially pure.
  • substantially pure refers to a compound of at least about 85%, by dry weight, of isolated fraction, or at least ''85% substantially pure.'' Most specifically, the term “substantially pure” refers to a compound of at least about 95%, by dry weight, of isolated fraction, or at least “95% substantially pure.”
  • the term “substantially pure” may also be used to modify a synthetically-made protein or compound of the invention, where, for example, the synthetic protein is isolated from the reagents and byproducts of the synthesis reaction(s).
  • pharmaceutical grade when referring to a peptide or compound of the invention, is a peptide or compound that is isolated substantially or essentially from components which normally accompany the material as it is found in its natural state, including synthesis reagents and by-products, and substantially or essentially isolated from components that would impair its use as a pharmaceutical.
  • a “pharmaceutical grade” peptide may be isolated from any carcinogen.
  • “pharmaceutical grade” may be modified by the intended method of administration, such as "intravenous pharmaceutical grade,” in order to specify a peptide or compound that is substantially or essentially isolated from any substance that would render the composition unsuitable for intravenous administration to a patient.
  • an "intravenous pharmaceutical grade” peptide may be isolated from detergents, such as SDS, and antibacterial agents, such as azide,
  • detergents such as SDS
  • antibacterial agents such as azide
  • isolated, purified or biologically pure refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state.
  • isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment.
  • An “isolated" region of a polypeptide refers to a region that does not include the whole sequence of the polypeptide from which the region was derived.
  • nucleic acid, protein, or respective fragment thereof has been substantially removed from its in vho environment so that it maj be manipulated by the skilled artisan, such as but not limited to, nucleotide sequencing, restriction digestion, site-directed mutagenesis, and subcloning into expression vectors for a nucleic acid fragment as well as obtaining the protein or protein fragment in substantially pure quantities.
  • variant refers to amino acid sequence variants which may have amino acids replaced, deleted, or inserted as compared to the wild-type polypeptide. Variants may be truncations of the wild-type peptide. A “deletion' ' is the removal of one or more amino acids from within the polypeptide, which a “truncation” is the removal of one or more amino acids from one or both ends of the polypeptide.
  • a variant peptide may be made by manipulation of genes encoding the polypeptide.
  • a variant may be made by altering the basic composition or characteristics of the polypeptide, but not at least some of its pharmacologic activities.
  • a "variant" of azurin can be a mutated azurin that retains its ability to inhibit the development of premalignant mammalian cells.
  • a variant peptide is synthesized with non- natural amino acids, such as ⁇ -(3,5-dinitrobenzoyl)-Lys residues. Ghadiri & Fernholz, J. Am. Chem. Soc., 112:9633-9635 (1990).
  • the variant has not more than 20 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. In some embodiments, the variant has not more than 15 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof.
  • the variant has not more than 10 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. In some embodiments, the variant has not more than 6 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. In some embodiments, the variant has not more than 5 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. In some embodiments, the variant has not more than 3 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof.
  • the term ''amino acid means an amino acid moiety that comprises any naturally-occurring or non-natural Iy occurring or synthetic amino acid residue, i.e.. any moiety comprising at least one carboxyl and at least one amino residue directly linked b> one. two three or more carbon atoms, typically one ( ⁇ ) carbon atom.
  • a "derivative" of azu ⁇ n can, for example, be a chemically modified azurin that retains its ability to inhibit angiogenesis in mammalian cells.
  • Chemical modifications of interest include, but are not limited to. amidation, acetylation, sulfation, polyethylene glycol (PEG) modification, phosphorylation or glycosylation of the peptide.
  • a derivative peptide may be a fusion of a polypeptide or fragment thereof to a chemical compound, such as but not limited to, another peptide, drug molecule or other therapeutic or pharmaceutical agent or a detectable probe.
  • percent (%) amino acid sequence identity is defined as the percentage of amino acid residues in a polypeptide that are identical with amino acid residues in a candidate sequence when the two sequences are aligned. To determine % amino acid identity, sequences are aligned and if necessary, gaps are introduced to achieve the maximum % sequence identity; conservative substitutions are not considered as part of the sequence identity. Amino acid sequence alignment procedures to determine percent identity are well known to those of skill in the art. Often publicly available computer software such as BLAST, BLAST2, ALIGN2 or Megalign (DNASTAR) software is used to align peptide sequences. In a specific embodiment, Blastp (available from the National Center for Biotechnology Information, Bethesda MD) is used using the default parameters of long complexity filter, expect 10, word size 3, existence 11 and extension 1.
  • % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B can be calculated as:
  • % amino acid sequence identity XY* 100 where X is the number of amino acid residues scored as identical matches by the sequence alignment program's or algorithm's alignment of A and B and
  • Y is the total number of amino acid residues in B
  • the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A.
  • the shorter sequence will be the "B" sequence.
  • the truncated peptide will be the "B" sequence
  • the present invention provides compositions comprising cupredoxm, and variants, derivatives and structural equivalents of cupredoxins, and methods to prevent the development of cancer in mammals.
  • the invention also provides to variants, derivatives and structural equivalents of cupredoxin that retain the ability to prevent the development of cancer or the re-occurrence of cancer in mammals.
  • the invention provides compositions comprising Pseudomonas aeruginosa azu ⁇ n, variants, derivatives and structural equivalents of azurin, and their use to treat patients, and particularly patients at a higher risk of developing cancer than the general population.
  • the invention provides methods to study the development of cancer in mammalian cells, tissues and animals by contacting the cells with a cupredoxin, or variant, derivative or structural equivalent thereof, before or after inducing premalignant lesions, and observing the development of premalignant and/or malignant cells.
  • a cupredoxin or variant, derivative or structural equivalent thereof
  • a redox protein elaborated by Pseudomonas aerugisnosa ⁇ the cupredoxin azurin selectively enters J774 lung cancer cells but not normal cells, and induces apoptosis. Zaborina et al, Microbiology 146:2521-2530 (2000).
  • Azurin can also selectively enter and kill human melanoma UISO-Mel-2 or human breast cancer MCF-7 cells. Yamada et al, PNAS 99:14098-14103 (2002); Punj et al., Oncogene 23:2367- 2378 (2004). Azurin from P, aeruginosa preferentially enters J774 murine reticulum cell sarcoma cells, forms a complex with and stabilizes the tumor suppressor protein p53, enhances the intracellular concentration of p53, and induces apoptosis. Yamada et al.. Infection and Immunity 70:7054-7062 (2002).
  • amino acids 50-77 (p28) (SEQ ID NO: 2) represented a protein transduction domain (PTD) critical for internalization and subsequent apoptotic activity.
  • PTD protein transduction domain
  • azurin, and peptides derived from azurin, such as p28 and pi 8. have chemopreventive properties. It is now known that azurin, p28. prevent formation of premalignant preneoplastic lesions in mouse mammary" gland organ culture. In a mouse mammary gland organ culture model, azurin at 50 ⁇ g/ml was found to inhibit the formation of alveolar lesions by 6 "70 o. Likewise, p2S at 25 ⁇ g/ml was found to inhibit the formation of alveolar lesions by 67° ⁇ .
  • Example L Further, azu ⁇ ri at 50 ⁇ g ml was found to inhibit the formation of ductal lesions by 79%, and p28 at 25 ⁇ g/ml inhibited the formation of ductal lesions by 71%.
  • Example 1 Confocal microscopy and FAC showed that azurin and p28 entered normal murine mammary epithelial cells (MM3MG) and mammary cancer cells (4Tl), P28 also entered human umbilical vein endothelial cells (HUVEC) in a temperature. time and concentration dependent manner and inhibited capillary tube formation of HUVEC plated on Matrigei* ' in a dose dependent manner.
  • Standard cancer treatment methods involve damaging the DNA of the cancer cell.
  • the cellular response to normal DNA damage includes activation of DNA repair, cell cycle arrest and lethality (Hall, Radiobiology jor the Radiologist, Harper and Row, 1988).
  • Hall Radiobiology jor the Radiologist, Harper and Row, 1988.
  • the induction of DNA double-strand breaks results in lethal chromosomal aberrations that include deletions, dicentrics, rings, and anaphase bridges (Hall, Radiobiology for the Radiologist, Harper and Row, 1994).
  • pi 8 may have use as a non- viral vector for introducing materials into tumors and cancer cells.
  • the peptides of the present invention may be used to introduce DNA or RKA fragments into a cancer cell thereby providing a therapeutic DNA or RNA fragment treatment to a tumor or cancer cell.
  • RNAi approaches hematopoietic gene transfer, homologous recombination, ribozyme technology, antisense technology, tumor immunotherapy and tumor suppressors, translational research, anti-gene therapy (antisense, siRNA & ribozymes), apoptosis, immunology and immunotherapy, DNA synthesis and repair.
  • Gene therapy involves the transfer of a foreign gene into a cancer cell, for example a tumor suppressor or inducer of apoptosis, under conditions suitable for expression of the gene. Once expressed, the gene product confers a beneficial effect on the tumor cell by either slowing its growth, inhibiting its metastatic potential, or killing it outright.
  • a cancer cell for example a tumor suppressor or inducer of apoptosis
  • the gene product confers a beneficial effect on the tumor cell by either slowing its growth, inhibiting its metastatic potential, or killing it outright.
  • the compounds of the present invention address the selective targeting of tumor cells.
  • several strategies have been proposed for the control of gene expression.
  • One strategy is transcriptional targeting in which the promoter regulating the therapeutic gene is activated by tumor- selective transcription factors.
  • Examples include the use of the MUC-I promoter in breast cancer and the CEA promoter in colon cancer (Kurihara et ai, "Selectivity of a replication- component adenovirus for human breast carcinoma cells expressing the MUCl antigen," J. Clin. Invest. 106(6): 763-771, 2000; Konishi et aL, "Transcriptionally targeted in vivo gene therapy for carcinoembrionic antigen-producing adenocarcinoma,” J. Med. ScL, 48(3): 79-89, 1999).
  • Antisense techniques rely on the introduction of a nucleic acid molecule into a cell which typically is complementary to a mRNA expressed by the selected gene.
  • the antisense molecule typically suppresses translation of the mRNA molecule and prevents the expression of the polypeptide encoded by the gene. Modifications of the antisense technique may prevent the transcription of the selected gene by the antisense molecule binding to the gene's DNA to form a triple helix.
  • One particular antisense drug that can be used in accordance with the present invention is G3139 (also known as oblimersen; manufactured by Genta. Inc., Lexington, MA).
  • Another particular antisense molecule that can be used is G4460 (also known as c-myb antisense manufactured by Genta, Berkeley Heights, NJ).
  • RNA interference (RNAi) based molecules can also be attached to the peptides of the present invention.
  • RNAi is generally mediated b> double stranded RNA ("dsRNA”), short hairpin RNA (“shRNA”) or other nucleic acid molecules with similar characteristics.
  • dsRNA double stranded RNA
  • shRNA short hairpin RNA
  • RISC complex protein complex
  • the RISC complex will degrade mRNA that complementariiy base pairs with the nucleic acid molecules it has taken up. In this manner, the mRNA is specifically destroyed, thus preventing encoded-for proteins from being made.
  • Ribozyme technologies rely on the introduction of a nucleic acid molecule into a cell which expresses a RKA molecule which binds to, and catalyses the selective cleavage of, a target RNA molecule.
  • the target RKA molecule is typically a mRNA molecule, but it may be, for example, a retroviral RNA molecule.
  • Targeted gene deletion by homologous recombination, which requires two gene- inactivating events (one for each allele) is also a strategy that can be used with the present invention.
  • Particular therapies delivered in conjunction with the compounds of the present invention can also be directed against cancer-specific transcription complexes (CSTCs) that can control expression of proteins that are critical for cancer development. See, for example. United States Patent Application No. 2008/0027002 which is incorporated by reference herein for its teachings regarding cancer therapies directed against CSTCs.
  • CSTCs cancer-specific transcription complexes
  • cupredoxins Due to the high degree of structural similarity between cupredoxins, it is likely that other cupredoxins will inhibit the formation of premalignant lesions in mammals as well as azurin. Such cupredoxins may be found in, for example, bacteria or plants.
  • cupredoxins are known to have pharmacokinetic activities similar to those of azurin from Pseudomonas aeruginosa.
  • rusticyanin from Thiobacillus ferrooxidans can also enter macrophages and induce apoptosis.
  • Yamada et al, Cell. Micro. 7:1418-1431 (2005) Yamada et al, Cell. Micro. 7:1418-1431 (2005).
  • cupredoxins from Phormidium laminosum and pseudoazurin form ⁇ chromobacter cycloclastes also are cytotoxic towards macrophages.
  • U.S. Pat. Pub. No. 20060040269, published Feb. 23, 2006 It is therefore contemplated that other cupredoxins may be used in the compositions and methods of the invention.
  • variants, derivatives, and structural equivalents of cupredoxins that retain the ability to inhibit the formation of cancer in mammals may also be used in the compositions and methods of the invention. These variants and derivatives may include, but are not limited to, truncations of a eupredoxin. conservative substitutions of amino acids and proteins modifications such as PEGylation and all-hydrocarbon stabling of ⁇ -helices Compositions of the Invention
  • the invention provides for peptides that are variants, derivatives or structural equivalents of eupredoxin that inhibit the development of premalignant lesions in mammalian cells, tissues and animals.
  • the invention further provides for peptides that are variants, derivatives or structural equivalents of eupredoxin that inhibit the development of cancer in mammalian cells, tissues and animals.
  • the peptide is isolated.
  • the peptide is substantially pure or pharmaceutical grade,
  • the peptide is in a composition that comprises, or consists essentially of, the peptide.
  • the peptide is non-antigenic and does not raise an immune response in a mammal, and more specifically a human.
  • the peptide is less that a full-length eupredoxin, and retains some of the pharmacologic activities of the cupredoxins. Specifically, in some embodiments, the peptide may retain the ability to inhibit the development of premalignant lesions in the mouse mammary gland organ culture.
  • the invention also provides compositions comprising at least one peptide that is a eupredoxin, or variant, derivative or structural equivalent of a eupredoxin, specifically in a pharmaceutical composition.
  • the pharmaceutical composition is designed for a particular mode of administration, for example, but not limited to, oral, intraperitoneal, or intravenous. Such compositions may be hydrated in water, or may be dried (such as by lyophilization) for later hydration. Such compositions may be in solvents other than water, such as but not limited to, alcohol.
  • compositions comprising peptides that are variants, derivatives or structural equivalents of eupredoxin that selectively enter cancer cells and/or tumors in mammalian cells, tissues and animals.
  • the peptide is pi 8 having SEQ ID NO. 25.
  • the peptide is a variant, derivative or structural equivalent of pi 8.
  • the composition is pi 8 coupled to DNA or RNA.
  • the DNA or RNA is a gene or a portion of a gene.
  • the DNA or RNA has a therapeutic effect once delivered.
  • cupredoxins will have the same chemopre ⁇ e ⁇ tive properties as azurin and p28.
  • the cxipredoxin is. but is not limited to. azurin, pseudoa/urin, plastocyanin. rusticyanin. auracya ⁇ in. steliacyamn, cucumber basic protein or La/.
  • the azurin is derived from Pseudomonas aeruginosa, Alcaligenes jaecalis, ⁇ chromobacter xylosoxidans ssp.denitrificans L Bordetella bronchiseptica ⁇ Methylomonas sp., Neisseria meningitidis, Neisseria gonorrhea, Pseudomonas fluorescens, Pseudomonas chlororaphis , Xylella fastidiosa, U ⁇ va pertussis or Vibrio parahaemol ⁇ ticm, In a very specific embodiment, the azurin is from Pseudomonas aeruginosa, In other specific embodiments, the cupredoxin comprises an amino acid sequence that is SEQ ID KO: 1 , 3-19.
  • the invention provides peptides that are amino acid sequence variants which have amino acids replaced, deleted, or inserted as compared to the wild-type cupredoxin. Variants of the invention may be truncations of the wild-type cupredoxin. In some embodiments, the peptide of the invention comprises a region of a cupredoxin that is less that the full length wild-type polypeptide. In some embodiments, the peptide of the invention comprises more than about 10 residues, more than about 15 residues or more than about 20 residues of a truncated cupredoxin.
  • the peptide comprises not more than about 100 residues, not more than about 50 residues, not more than about 40 residues, not more than about 30 residues or not more than about 20 residues of a truncated cupredoxin.
  • a cupredoxin has to the peptide, and more specifically SEQ ID NOS: 1, 3-19 as to the peptide of the invention, at least about 70% amino acid sequence identity, at least about 80% amino acid sequence identity, at least about 90% amino acid sequence identity, at least about 95% amino acid sequence identity or at least about 99% amino acid sequence identity.
  • the variant of cupredoxin comprises P.
  • the variant of cupredoxin consists of P. aeruginosa azurin residues 50-77 (SEQ ID NO: 2), azurin residues 50-67 (SEQ ID NO: 25), or azurin residues 36-88 (SEQ ID NO: 26).
  • the variant consists of the equivalent residues of a cupredoxin other that azurin.
  • cupredoxin variants can be designed that a simitar pharmcologic activity to azurin residues 50-77 (SEQ ID NO: 2), or azurin residues 36-88 (SEQ ID NO: 26).
  • the subject cupredoxin amino acid sequence will be aligned to the Pseudomonas aeruginosa azurin sequence using BLAST, BLAST2, ALIGN2 or Mega ⁇ gn (DNASTAR), the relevant residues located on the P. aeruginosa azurin amino acid sequence, and the equivalent residues found on the subject cupredoxin sequence, and the equivalent peptide thus designed.
  • the cupredoxin variant contains at least amino acids 57 to 89 of auracyanin B of Chloroflexus auraniiacus (SEQ ID NO: 20). In another embodiment, the cupredoxin variant contains at least amino acids 50-67 of Pseudomonas aeruginosa azurin (SEQ ID NO 25). In another embodiment of the invention, the cupredoxin variant contains at least amino acids 51 -T of Pseudomonas syringae azurin (SEQ ID NO: 21). In another embodiment of the invention, the cupredoxin variant contains at least amino acids 89-1 15 of Neisseria meningitidis Laz (SEQ ID NO: 22).
  • the cupredoxin variant contains at least ammo acids 52-78 of Vibrio parahaemolyticits azurin (SEQ ID NO: 23). In another embodiment of the invention, the cupredoxin variant contains at least amino acids 51-77 oiBordetella bronchiseptica azurin (SEQ ID NO: 24).
  • the variants may also include peptides made with synthetic amino acids not naturally occurring.
  • non-naturally occurring amino acids may be integrated into the variant peptide to extend or optimize the half-life of the composition in the bloodstream.
  • variants include, but are not limited to. D,L-peptides (diastereomer), (for example
  • the peptide of the invention is a derivative of a cupredoxin.
  • the derivatives of cupredoxin are chemical modifications of the peptide such that the peptide still retains some of its fundamental activities.
  • a "derivative" of azurin can be a chemically modified azurin that retains its ability to inhibit the development of prema ⁇ gnant lesions in mammalian cells, tissues or animals.
  • Chemical modifications of interest include, but are not limited to, hydrocarbon stabling, amidation, aeety ⁇ atioFL sulfation, polyethylene glycol (PEG) modification, phosphorylation and glycosylation of the peptide.
  • a derivative peptide maybe a fusion of a cupredoxin, or variant, derivative or structural equivalent thereof to a chemical compound, such as but not limited to. another peptide, drug molecule or other therapeutic or pharmaceutical agent or a detectable probe
  • Derivatives of interest include chemical modifications bv which the half-life in the bloodstream of the peptides and compositions of the invention can be extended or optimized, such as by several methods well known to those in the art, including but not limited to, circularized peptides (for example Monk et aL BioDrugs 19(4):261-78, (2005); DeFreest et ah, J. Pept. Res.
  • the peptide is a structural equivalent of a cupredoxin.
  • studies that determine significant structural homology between cupredoxins and other proteins include Toth et al. (Developmental Cell 1 :82-92 (2001 )).
  • significant structural homology between a cupredoxin and the structural equivalent may be determined by using the VAST algorithm. Gibrat et al, Curr Opin Struct Biol 6:377-385 (1996); Madej et al, Proteins 23:356-3690 (1995).
  • the VAST p value from a structural comparison of a cupredoxin to the structural equivalent may be less than about 10 ⁇ 3 , less than about 10 " ⁇ or less than about 10 "7 .
  • significant structural homology between a cupredoxin and the structural equivalent may be determined by using the DALI algorithm. Holm & Sander, J. MoI. Biol. 233:123-138 (1993).
  • the DALI Z score for a pairwise structural comparison is at least about 3.5, at least about 7.0, or at least about 10.0.
  • the peptides of the composition of invention may be more than one of a variant, derivative and/or structural equivalent of a cupredoxin.
  • the peptides may be a truncation of azurin that has been PEGylated, thus making it both a variant and a derivative.
  • the peptides of the invention are synthesized with ⁇ . ⁇ - disubstituted non-natural amino acids containing olef ⁇ n-bearing tethers, followed by an all- hydrocarbon " 'staple" by ruthenium catalyzed olefin metathesis.
  • peptides that are structural equivalents of azurin may be fused to other peptides, thus making a peptide that is both a structural equivalent and a derivative.
  • Variants, derivatives or structural equivalents of cupredoxin may or may not bind copper.
  • the cupredoxin. or variant, derivative or structural equivalent thereof has some of the pharmacologic activities of the P aeruginosa azurin, and specifically
  • cupredoxins and variants, derivatives and structural equivalents of cupredoxins that may inhibit prevent the development of premalignant lesions in mammalian cells, tissues or animals, and specifically but not limited to. mammary gland cells.
  • the invention also provides for the cupredoxins and variants, derivatives and structural equivalents of cupredoxins that may have the ability to inhibit the development of mammalian premahgnant lesions, and specifically but not limited to. melanoma, breast, pancreas, glioblastoma, astrocytoma, lung, colorectal, neck and head, bladder, prostate, skin and cervical cancer cells.
  • Inhibition of the development of cancer cells is any decrease, or lessening of the rate of increase, of the development of premalignant lesions that is statistically significant as compared to control treatments.
  • cupredoxins can inhibit the development of premalignant lesions and ultimately cancer in mammalian cells, tissues or animals, and specifically breast cells, and more specifically, mouse mammary gland cells
  • variants and derivatives of cupredoxins that retain this chemopreventive activity.
  • Such variants, derivatives and structural equivalents can be made by, for example, creating a "library" of various variants, derivatives and structural equivalents of cupredoxins and cupredoxin derived peptides and then testing each for chemopreventive activity, and specifically chemopreventive activity in the mouse mammary gland organ culture using one of many methods known in the art, such the exemplary method in Example 1. It is contemplated that the resulting variants, derivatives and structural equivalents of cupredoxins with chemopreventive activity may be used in the methods of the invention, in place of or in addition to azurin or p28.
  • the variant, derivative or structural equivalent of cupredoxin may inhibit the development of 7,12-dimethylbenz (a) anthracene (DMBA) induced premalig ⁇ ant lesions in a mouse mammary gland organ culture (MMOC) to a degree that is statistically different from a non-treated control,
  • DMBA 7,12-dimethylbenz
  • MMOC mouse mammary gland organ culture
  • a peptide can be tested for this activity by using the MMOC model system is desc ⁇ bed m Example 1 , or as in Mehta et al (J Natl Cancer Inst 93: 1 103-1106 (2001 )) and Mehta e/ ⁇ /, (Meth Cell Sci 19:19-24 (199?)).
  • Other methods to determine whether cancer development is inhibited another are well known in the art and may be used as well,
  • the derivative or structural eqimalent of cupredoxin inhibits the dev elopment of mammary alveolar lesions (MAI ) in the a M 1 VlOC model to a degree that is statistically different from a non-treated control.
  • the variant, de ⁇ vative or structural equivalent of cupredoxin inhibits the development of mammary ductal lesions (MDL) in the a MMOC model to a degree that is statistically different from a non-treated control.
  • MDL mammary ductal lesions
  • a peptide can be tested for these activities by using the MMOC model system induced to form premalignant lesions by DMBA, as described in Example 1. Evaluation of development of premalignant lesions in a MMOC model system may be determined by morphometic analysis, or histopathological analysis, as provided in Example 1 ,
  • the variant, derivative or structural equivalent can selectively enter cancer cells and/or tumors in mammalian cells, tissues and animals.
  • the variant is a derivative or structural equivalent of pi 8.
  • the variant, derivative or structural equivalent can selectively enter cancer cells andor tumors in mammalian cells, tissues and animals and deliver DNA or RNA.
  • the DNA or RNA is a gene or a portion of a gene. In some embodiments, the DNA or RNA has a therapeutic effect once delivered.
  • cupredoxins small blue copper proteins
  • the copper ion is solely bound by the protein matrix.
  • a special distorted trigonal planar arrangement to two histidine and one cysteine ligands around the copper gives rise to very peculiar electronic properties of the metal site and an intense blue color.
  • a number of cupredoxins have been crystallographically characterized at medium to high resolution. The cupredoxins in general have a low sequence homology but high structural homology. Gough & Clothia, Structure 12:917-925 (2004); De Rienzo et al. Protein Science 9: 1439-1454 (2000).
  • amino acid sequence of azurirt is 31% identical to that of auracyamn B. 16.3% to that of rustic ⁇ anin, 20.3 % to that of plastoc ⁇ anm, and 17.3% to that of pseudoazurin. See, Table 1. However, the structural similarity of these proteins is more pronounced.
  • the VAST p value for the comparison of the structure of azurin to auracyanin B is 10 " ' " ⁇ azurin to rusticyanin is 10 ⁇ s , azurin to plastocyan ⁇ n is IG ⁇ 6 , and azurin to psuedoazurin is W 4 ⁇ All of the cupredoxins possess an eight-stranded Greek key beta-barrel or beta- sandwich fold and have a highly conserved site architecture, De Rienzo et at., Protein Science 9: 1439-1454 (2000), A prominent hydrophobic patch, due to the presence of many long chain aliphatic residues such as methionines and leucines, is present around the copper site in az ⁇ rins, amicyanins, cyanobacterial plastocyanins, cucumber basic protein and to a lesser extent, pseudeazurm and eukaryotic plastocyanins. Id. Hydrophobic patches are also
  • VAST p value is a measure of the significance of the comparison, expressed as a probability. For example, if the p value is 0.00 L then the odds are 1000 to 1 against seeing a match of this quality by pure chance.
  • the p value from VAST is adjusted for the effects of multiple comparisons using the assumption that there arc 500 independent and unrelated t>pes of domains in the MMDB database. The p value shown thus corresponds to the p value for the pairwise comparison of each domain pair, divided by 500.
  • VAST structure-similarity score The VAST structure-similarity score. This number is related to the number of secondary structure elements superimposed and the quality of that superposition. Higher VAST scores correlate with higher similarity,
  • RMSD The root mean square superposition residual in Angstroms. This number is calculated after optimal superposition of two structures, as the square root of the mean square distances between equivalent C-alpha atoms. Note that the RJVlSD value scales with the extent of the structural alignments and that this size must be taken into consideration when using RMSD as a descriptor of overall structural similarity.
  • the azurins are copper containing proteins of 128 amino acid residues which belong to the family of cupredoxins involved in electron transfer in certain bacteria.
  • the azurins include those from P. aeruginosa (PA) (SEQ ID NO: 1), A. xylosoxidans, and A. denitrificans. Murphy et ai, J. MoL Biol. 315:859-871 (2002).
  • PA P. aeruginosa
  • the amino acid sequence identity between the azurins varies between 60-90%, these proteins showed a strong structural homology. All azurins have a characteristic ⁇ -sandwich with Greek key motif and the single copper atom is always placed at the same region of the protein.
  • azurins possess an essentially neutral hydrophobic patch surrounding the copper site. Id.
  • PIastocyanins are soluble proteins of cyanobacteria, algae and plants that contain one molecule of copper per molecule and are blue in their oxidized form. They occur in the ehtor ⁇ plast where they function as electron carriers. Since the determination of the structure of poplar plastocyanin in 1978, the structure of algal (Scenedesmus, Enteromorpha, Chlamydomonas) and plant ⁇ French bean) plastocyanms has been determined either by crystal Iographic or NMR methods, and the poplar structure has been refined to 1,33 A resolution. SEQ ID NO: 3 shows the amino acid sequence of plastocyanin from Phormidium laminosum..
  • thermophilic cyanobactcrium Another plastocyanin of interest is from Viva pertussis. Despite the sequence divergence among plastocyanins of algae and vascular plants (e.g., 62% sequence identity between the Chlamydomonas and poplar proteins), the three- dimensional structures are conserved (e.g., 0.76 A rms deviation in the C alpha positions between the Chlamydomonas and Poplar proteins). Structural features include a distorted tetrahedral copper binding site at one end of an eight- stranded antiparallel beta-barrel, a pronounced negative patch, and a flat hydrophobic surface.
  • the copper site is optimized for its electron transfer function, and the negative and hydrophobic patches are proposed to be involved in recognition of physiological reaction partners.
  • Chemical modification, cross- linking, and site-directed mutagenesis experiments have confirmed the importance of the negative and hydrophobic patches in binding interactions with cytochrome f , and validated the model of two functionally significant electron transfer paths involving plastocyanin.
  • One putative electron transfer path is relatively short (approximately 4 A) and involves the solvent-exposed copper ligand His-87 in the hydrophobic patch, while the other is more lengthy (approximately 12-15 A) and involves the nearly conserved residue Tyr-83 in the negative patch. Redinbo et at, J. Bioenerg. Biomembr. 26:49-66 (1994).
  • Rusticyanins are blue-copper containing single-chain polypeptides obtained from a Thiobacilhts (now called Acidithiobacillus).
  • the X-ray crystal structure of the oxidized form of the extremely stable and highly oxidizing cupredoxin rusticyanin from Thiobacillus ferrooxidans (SEQ ID NO: 4) has been determined by multiwavelength anomalous diffraction and refined to 1.9 A resolution.
  • the rusticyanins are composed of a core beta- sandwich fold composed of a six- and a seven-stranded b-sheet.
  • the copper ion is coordinated by a cluster of four conserved residues (His 85, Cysl38. Hisl43, Met 148) arranged in a distorted tetrahedron. Walter, RX. et at. J. MoI. Biol. 263:730-51 (1996).
  • the pseudoazurins are a family of blue-copper containing single-chain polypeptide.
  • the amino acid sequence of pseudoazurin obtained from Achromobacter cyctoclastes is shown in SEQ ID XO: 5.
  • the X-ray structure analysis of pseudoazurin stums that it has a similar structure to the a/unns although there i ⁇ low sequence homology between these proteins. Two main differences exist between the overall structure of the pseudoazurins and azurins.
  • the proteins identifiable as phytocyanins include, but are not limited to, cucumber basic protein, stellacyanin, mavicyanin, umecyanin, a cucumber peeling cupredoxin, a putative blue copper protein in pea pods, and a blue copper protein from Arabidopsis thal ⁇ ana. hi all except cucumber basic protein and the pea-pod protein, the axial methionine ligand normally found at blue copper sites is replaced by glutamine.
  • auracyanin A Three small blue copper proteins designated auracyanin A.
  • auracyanin B-I, and auracyanin B-2 have been isolated from the thermophilic green gliding photosynthetic bacterium Chloroflexus aurantiacus.
  • the two B forms are glycoproteins and have almost identical properties to each other, but are distinct from the A form.
  • the sodium dodecyl sulfate-polyacryl amide gel electrophoresis demonstrates apparent monomer molecular masses as 14 (A), 18 (B-2). and 22 (B-I) kDa.
  • auracyanin A The amino acid sequence of auracyanin A has been determined and showed auracyanin A to be a polypeptide of 139 residues. Van Dreissehe ct al, Protein Science 8:947-957 (1999). His58, Cysl23. Hisl28, and Metl 32 are spaced in a way to be expected if they are the evolutionary conserved metal Iigands as in the known small copper proteins plastocyanm and azurin. Secondary structure prediction also indicates that auracyanin has a general beta-barrel structure similar to thai of azurin from Pseudomonas aeruginosa and plastocyariin from poplar leaves. However, auracyanin appears to have sequence characteristics of both small copper protein sequence classes.
  • the overall similarity with a consensus sequence of azurin is roughly the same as that with a consensus sequence of plastoeyanin, namely 30 5%.
  • the N -terminal sequence region I - 18 of auracyanin is remarkably nch in glycine and hydroxy ammo acids.
  • the auracyanin B molecule has a standard cupredoxin fold.
  • the crystal structure of auracyanin B from Chloroflexus aurantiacus has been studied. Bond et al, J. MoI. Biol. 306:47-67 (2001). With the exception of an additional N-terminal strand, the molecule is very similar to that of the bacterial cupredoxin, azurin.
  • one of the Cu iigands lies on strand 4 of the polypeptide, and the other three lie along a large loop between strands 7 and 8. The Cu site geometry is discussed with reference to the amino acid spacing between the latter three Iigands.
  • the crystallographically characterized Cu-binding domain of auracyanin B is probably tethered to the periplasmic side of the cytoplasmic membrane by an N-terminal tail that exhibits significant sequence identity with known tethers in several other membrane-associated electron-transfer proteins.
  • the amino acid sequences of the B forms are presented in McManus et al. J. Biol. Chem. 267:6531-6540 (1992). See exemplary amino acid sequence SEQ ID NO: 16 for chain B of auracyanin from Chloroflexus aurantiacus (NCBI Protein Data Bank Accession No. IQHQA).
  • Stellacyanins are a subclass of phytocyanins, a ubiquitous family of plant cupredoxins.
  • An exemplary sequence of a stellacyanin is included herein as SEQ ID NO: 14.
  • the crystal structure of umecyanm, a stellacyanin from horseradish root (Koch et al, J. Am. Chem. Soc. 127:158-166 (2005)) and cucumber stellacyanin (Hart el al. Protein Science 5:2175-2183 (1996)) is also known.
  • the protein has an overall fold similar to the other phytocyanins.
  • the ephrin B2 protein ectodomain tertiary structure bears a significant similarity to stellacyanin. Toth et al, Developmental CeU 1 :83-92 (2001).
  • An exemplary amino acid sequence of a stellacyanin is found in the National Center for Biotechnology Information Protein Data Bank as Accession No. IJER, SEQ ID NO
  • An exemplary amino acid sequence from a cucumber basic protein is included herein as SEQ ID NO: 17,
  • the crystal structure of the cucumber basic protein (CBP). a type 1 blue copper protein, has been refined at 1.8 A resolution. The molecule resembles other blue copper proteins in having a Greek key beta-barrel structure, except that the barrel is open on one side and is better described as a "beta-sandwich " ' or "beta-taco”. Guss et al, J. MoI. Biol. 262:686-705 (1996).
  • the ephrinB2 protein ectodomian tertiary structure bears a high similarity (rms deviation 1.5A for the 50 ⁇ carbons) to the cucumber basic protein. Toth et al, Developmental Cell 1 :83-92 (2001).
  • the Cu atom has the normal blue copper NNSS' co-ordination with bond lengths Cu-
  • a disulphide link, (Cys52)-S-S-(Cys85) appears to play an important role in stabilizing the molecular structure.
  • the polypeptide fold is typical of a sub-family of blue copper proteins (phytocyanins) as well as a non-metalloprotein, ragweed allergen Ra3, with which CBP has a high degree of sequence identity.
  • the proteins currently identifiable as phytocyanins are CBP, stellacyanin, mavicyanin, umecyanin, a cucumber peeling cupredoxin, a putative blue copper protein in pea pods, and a blue copper protein from Arabidopsis thaliana.
  • CBP CBP
  • stellacyanin mavicyanin
  • umecyanin a cucumber peeling cupredoxin
  • a putative blue copper protein in pea pods a putative blue copper protein in pea pods
  • a blue copper protein from Arabidopsis thaliana In all except CBP and the pea-pod protein, the axial methionine ligand normally found at blue copper sites is replaced by glutamine.
  • An exemplary sequence for cucumber basic protein is found in NCBI Protein Data Bank Accession No. 2CBP, SEQ ID NO: 17.
  • the invention provides methods to prevent de novo malignancies in otherwise healthy patients comprising administering to the patient at least one peptide that is a cupredoxin, or variant, derivative or structural equivalent thereof, as described above.
  • Chemopreventive therapies are based on the hypothesis that the interruption of processes involved in cancergenesis will prevent the development of cancer.
  • the cupredoxin Pseudomonas aeruginosa azurin and the truncated azurin peptide p28 are now known to inhibit the development of premalignant lesions, either by inhibiting the initial formation of premalignant lesions, or killing or inhibiting the growth of premalignant lesions that are present. It therefore contemplated that a cupredoxin.
  • cancers that may be prevented by treatment with the compositions of the invention include, but are not limited to, melanoma, breast, pancreas, glioblastoma, astrocytoma, lung, colorectal, neck and head, bladder, prostate, skin, and cervical cancer.
  • the patient may be human. In other embodiments, the patient is not human.
  • the invention further includes methods to study the development of cancer comprising contacting mammalian cells before or after induction with a carcinogen with a composition comprising cupredoxin, or a variant, derivative or structural equivalent thereof and observing the development of the cells.
  • the cells are mouse mammary gland cells, while in others they are other cells that may become malignant in mammals.
  • Patients at a higher at risk to develop cancer than the general population may be patients with high risk features, patients with premalignant lesions, and patients that have been cured of their initial cancer or definitively treated for their premalignant lesions. See generally Tsao et al, CA Cancer J Clin 54: 150-180 (2004).
  • High risk features may be behavioral, genetic, environmental or physiological factors of the patient. Behavioral factors that predispose a patient to various forms of cancer include, but are not limited to, smoking, diet, alcohol consumption, hormone replacement therapy, higher body mass index, nulliparity, betal nut use, frequent mouthwash use, exposure to human papillomavirus, childhood and chronic sun exposure, early age of first intercourse, multiple sexual partners, and oral contraceptive use.
  • Genetic factors that predispose a patient to various forms of cancer include, but are not limited to, a family history of cancer, gene carrier status of BRCAl and BRCA2, prior history of breast neoplasia, familial adenomatous polyposis (FAP), hereditary nonpolyposis colorectal cancer (HNPCC), red or blond hair and fair-skinned phenotype, xeroderma pigmentosum, and ethnicity.
  • Environmental features that predispose a patient to various forms of cancer include, but are not limited to, exposure to radon, polycyclic aromatic hydrocarbons, nickel, chromate, arsenic, asbestos, chioromethyl ethers, benzo[a]pyrene.
  • miscellaneous factors that predispose a patient to various forms of cancer include, but are not limited to, chronic obstructive pulmonary disease with airflow obstruction, chronic bladder infections, schistosomiasis, older age. and immunocompromised status.
  • patients at a higher risk of developing cancer may be determined by the use of various risk models that have been developed for certain kinds of cancer.
  • patients predisposed to breast cancer may be determined using the Gail risk model, orthe Claus model among others. See Gail et al . J Natl Cancer Inst 81 :1879- 1886 (1989); Cuzick, Breast 12:405-411 (2003); Huang et a!.. Am J Epidemiol 151:703-714 (2000).
  • premallgnant lesions are at a higher risk to develop cancer than the general population.
  • the presence of premalignant lesions in or on a patient may be determined by many methods that are well known to those in the art.
  • Intermediate markers or biomarkers that originate from premalignant lesions may be measured in a patient to determine if the patient harbors premalignant lesions.
  • Chromosomal abnormalities occur in tumor cells and the adjacent histologicialiy normal tissues in the majority of cancer patients. Progression in chromosomal abnormalities parallels the phenotypic progression from premalignant lesion to invasive cancer. Thiberville et al, Cancer Res. 55:5133-5139 (1995).
  • chromosomal abnormalities associated with cancer may be used as intermediate markers to detect premalignant lesions in a patient.
  • Common chromosomal abnormalities associated with cancer include, but are not limited to, allelic deletions or loss of heterozygosity (LOH) in tumor suppressor genes such as 3p (FHIT and others), 9p (9p21 for 17p ⁇ 17pl3 for P 53 gene and others) and I3q (13ql4 for retinoblastoma gene Rb and others). Deletions in 3p and 9p are associated with smoking and the early stages of lung cancer, Mao et al, J. Natl. Cancer Inst. 89:857-862 (1997).
  • Deletions affecting 3p, 5q, 8p, 17p and 18q are common change in epithelial cancers. See generally Tsao et al, CA Clin. Cancer J. Clin. 54:153 (2004).
  • Other chromosomal mutations associated with cancer include those which activate oncogenes.
  • Oncogenes whose presence may be used as intermediate markers include, but are not limited to, Ras, c-myc, epidemral growth factor.
  • erb-B2 and cyclins E, Dl and BL See generally id, at 154.
  • genes up-regulated in premalignant cells and cancer cells may be up-regulated in premalignant cells and cancer cells.
  • Genes that may be up-regulated in premalignant cells include, but are not limited to, eyelooxygenases COX-I and COX-2. telomerase.
  • Other biomarkers of cancer cells, and some premalignant ceils include, but are not limited to, p53, epidermal growth factor receptor (GFR). proliferating cell nuclear antigen (PCNA).
  • a second primary tumor refers to a new primary cancer in a person with a history of cancer. Second primary tumors are the leading cause of mortality in head and neck cancer. Id. at 150. A second primary tumor is distinct from a metastasis in that the former originates de novo while the later originates from an existing tumor. Patients that have been cured of cancer or premalignant lesions of the breast, head and neck, lung, and skin are at a particularly high risk to develop second primary tumors.
  • compositions comprising a cupredoxin or variant, derivative or structural equivalent thereof can be administered to the patient by many routes and in many regimens that will be well known to those in the art.
  • the cupredoxin, or variant, derivative or structural equivalent thereof is administered intravenously, intramuscularly, sub cutaneous iy, topically, orally, or by inhalation.
  • the compositions may be administered to the patient by any means that delivers the peptides to the site in the patient that is at risk of developing cancer.
  • the cupredoxin or variant. derivative or structural equivalent thereof is administered intraveneously.
  • the methods may comprise co-administering to a patient one unit dose of a composition comprising a cupredoxin or a variant, derivative or structural equivalent of cupredoxin and one unit dose of a composition comprising another chemopreventive drug, in either order, administered at about the same time, or within about a given time following the administration of the other, for example, about one minute to about 6o minutes following the administration of the other drug, or about 1 hour to about 12 hours following the administration of the other drug.
  • Chemopreventive drugs of interest include, but are not limited to, tamoxifen, aromatase inhibitors such as letrozoie and anastrozole (Arimidex*)- retinoids such as N-[4-hydroxyphenyl] ret ⁇ amide (4-HPR, fenretinide), nonsteriodal antiinflammatory agents (NSAIDs) such as aspirin and sulindac, caveecoxib (CGX-2 inhibitori defluoromethyiornithing (DFMO). ursodeoxycholic acid. 3-hvdroxy-3- methylglutaryl coenzyme A reductase inhibitors. EKI-785 (EGFR inhibitor).
  • VEGF-receptor antibody to VEGF-receptor
  • cetuximab antibody to EGFR
  • retinoi such as vitamin A, beta-carotene, 13-cis retinoic acid, isotretinoin and retinyl palrmtate, ⁇ tocopherol f interferon, oncolytic adenovirus dl!520 (ONYX-015).
  • compositions for Facilitating Selective Entry of Compounds into Cancer Cells and Tumors are provided.
  • the present invention relates to methods and mate ⁇ als for delivering a cargo compound into a cell. Delivery of the cargo compound according to this invention is accomplished by the use of a suitable transport polypeptide. In one embodiment of the invention, the cargo compound is linked to the transport polypeptide.
  • Suitable transport peptides include a cupredoxin, or a fragment of a cupredoxin containing a "cupredoxin entry domain".
  • cupredoxin entry domain refers to a fragment of a cupredoxin that includes the amino sequence that is required for the entry of cupredoxin into a mammalian cancer cell.
  • Cargo compounds delivered by the present invention include, but are not limited to, proteins, lipoproteins, polypeptides, peptides, polysaccharides, nucleic acids, including KNA, DNA and anti-sense nucleic acids, dyes, fluorescent and radioactive tags, microparticles or nanoparticles, toxins, inorganic and organic molecules, small molecules, and drugs (for example, chemopreventive drugs).
  • the drugs and toxins kill tumor cells.
  • the cupredoxin is an azurin, such as azurin from Pseudomonas aeruginosa (SEQ ID NO: 1).
  • the cupredoxin is a plastocyanin, a rusticyanin, or a pseudoazu ⁇ n, among others.
  • the azurin is from Pseudomonas aeruginosa, Pseudomonas syringa.
  • a cargo compound is delivered to kill or retard cell cycle progression in a cell, such as a cancer cell.
  • a cancer cell can be, for example, an osteosarcoma cell, lung carcinoma cell, colon carcinoma cell, lymphoma cell. leukemia cell, soft tissue sarcoma cell or breast, liver, bladder or prostate carcinoma cell, among others.
  • the cargo compound can be a cell cycle control protein, such as p53; a cyclin- dependent kinase inhibitor, such as pi 6.
  • a suicide protein such as thymidine kinase or nitroreductase
  • a cytokine or other immunomodulatory protein such as interleukin 1 , interleukin 2 or granulocyte-macrophage colony stimulating factor (GM-CSF); or a toxin, such as Pseudomonas aeruginosa exotoxin A. among others.
  • GM-CSF granulocyte-macrophage colony stimulating factor
  • a toxin such as Pseudomonas aeruginosa exotoxin A. among others.
  • a biologically active fragment of one of the above classes of compounds is delivered.
  • the cargo compound is delivered in order to generate an image of the target tissue.
  • the target tissue can be a cancer and the cargo compound can be one commonly used to generate an image for detection by X-ray computed tomography (CT), Magnetic Resonance Imaging (MRI) and ultrasound.
  • CT computed tomography
  • MRI Magnetic Resonance Imaging
  • the cargo compound is a gamma ray or positron emitting radioisotope, a magnetic resonance imaging contrast agent, an X-ray contrast agent, or an ultrasound contrast agent.
  • the invention further includes methods of selectively introducing DNA or RNA into a mammalian cancer cell.
  • the DNA or RNA is the cargo compound.
  • the method includes providing pi 8 coupled to DNA or RNA and introducing the compound into the body of a mammal.
  • the DNA or RNA is a gene or a fragment of a gene.
  • the DNA or RNA has a therapeutic effect once introduced into a mammalian cell. Cupredoxin Entry Domain
  • cupredoxin proteins comprise a protein transduction domain, the cupredoxin entry domain, which facilitates the entry of linked cargo into mammalian cancer cells.
  • the entire cupredoxin protein can be used to facilitate the transport linked cargo selectively into cancer cells.
  • a portion of a cupredoxin can be used to transport linked cargo into cancer cells.
  • the cupredoxin entry domain consists of a region of a cupredoxin that is less that the full length wild-type protein.
  • the cupredoxin entry domain consists more than about 10 residues, about 15 residues or about 20 residues of a cupredoxin. In some embodiments, the cupredoxin entry domain consists of not more than about 50 residues, about 40 residues or about 30 residues of a cupredoxin. In some embodiments, the cupredoxin entry domain has at least about 90% amino acid sequence identity, at least about 95% amino acid sequence identity or at least about 99° ⁇ amino acid sequence identity to a cupredoxin. In some embodiments, the cupredoxm entry domain is a azitrin entry domain.
  • aazurin entry domain contains at least amino acids 50 to 77 of ' Pseudomonas aeruginosa azurm (SEQ ID NO: 2).
  • the cupredoxin entry domain contains at least amino acids 36 to 7" of Pseudomonas aeruginosa azurin (SEQ ID NO: 27).
  • the cupredoxin entry domain contains at least ammo acids 36 to 89 of Pseudomonas aeruginosa azurin (SEQ ID NO: 28).
  • the cupredoxin entry domain contains at least ammo acids 36 to 128 of Pseudomonas aeruginosa azurin (SEQ ID NO: 29). In yet another embodiment of the invention, the cupredoxin entry domain contains at least amino acids 50 to 67 of Pseudomonas aeruginosa azurin (SEQ ID NO: 25). In another embodiment of the invention, the cupredoxin entry domain contains at least amino acids 53 to 70 of Pseudomonas aeruginosa azurin (SEQ ID NO: 30).
  • the cupredoxin entry domain contains at least amino acids 53 to 64 of Pseudomonas aeruginosa azurin (SEQ ID NO: 31). In another embodiment of the invention, the cupredoxin entry domain is an entry domain from a cupredoxin other than P. aeruginosa azurin.
  • the cupredoxin entry domain maybe a fragment of plastocyanin from the cyanobacteriurn Phormidium laminosum (SEQ ID NO: 3), rusticyanin from Thiobacillus ferrooxidans (SEQ ID NO: 4); pseudoazurin from Achromobacter cycloclastes (SEQ ID NO: 5), azurin from Pseudomonas syringae (SEQ ID NO: 21), azurin from Neisseria meningitidis (SEQ ID NO: 10), azurin from Vibrio parahaemolyticus (SEQ ID NO: 8), or an auracyanin from Chloroflexus aurantiacus (SEQ ID NO: 15 and 16).
  • the cupredoxin entry domain contains at least amino acids 57 to 89 of auracyanin B of Chloroflexus aurantiacus (SEQ ID NO: 20).
  • the cupredoxm entrv domain contains at least ammo acids 51 -77 of Pseudomonas syringae azurm (S EQ ID NO: 21 ).
  • the cupredoxin entry domain contains at least amino acids 89-1 15 of Neisseria meningitidis h ⁇ ''L (SEQ ID NO: 22).
  • the cupredoxin entry domain contains at least amino acids 52-78 of Vibrio parahaemolyticus azurin (SEQ ID NO: 23). In another embodiment of the invention, the cupredoxm entry domain contains at least ammo acids 51 -77 of Bordelella bronchiscpnca azurin (SEQ ID NO: 24). Modification of a Cupredoxin Entry Domain
  • a cupredoxin entry domain is chemically modified or genetically attered to produce variants that retain the ability to transport a cargo compound into a cell.
  • Example 14 shows that Pseudomonas aeruginosa azurin having proline residues introduced at positions 54, 61 and 70 retains its ability to enter UISO-Mel-2 cells.
  • the cupredoxin entry domain comprises a conserved amino acid sequence DGXXXXDXXYXKXXD (SEQ ID NO: 32) or DGXXXXDXXYXKXXD (SEQ ID NO: 33) where D is aspartic acid, G is glycine, Y is tyrosine, K is lysine and X is any amino acid. See Example 17.
  • Variants of a cupredoxin entry domain may be synthesized by standard techniques.
  • Derivatives are amino acid sequences formed from native compounds either directly or by modification or partial substitution.
  • Analogs are amino acid sequences that have a structure similar, but not identical, to the native compound but differ from it in respect to certain components or side chains. Analogs may be synthesized or from a different evolutionary origin.
  • Variants may be full length or other than full length, if the derivative or analog contains a modified amino acid.
  • Variants of a cupredoxin entry domain include, but are not limited to, molecules comprising regions that are substantially homologous to the cupredoxin entry domain by at least about 65%, 70%, 75%. 85%, 90%. 95%, 98%, or 99% identity over an amino acid sequence of identical size or when compared to an aligned sequence in which the alignment is performed by a homology algorithm.
  • the variants of a cupredoxin entry domain have a significant structural similarity to P, aeruginosa azurin residues 50-77 (SEQ ID NO: 2). In other embodiments, the variants of a cupredoxin entry domain have a significant structural similarity to P. aeruginosa azurin residues 50-67 (SEQ ID NO: 25). Examples of studies that determine significant structural homology between cupredoxins and other proteins include Toth c( al. (Developmental Cell 1:82-92 (2001)). Specifically, significant structural homology between a variant of the cupredoxin entry domain and P.
  • aeruginosa azurin residues 50- ⁇ 7 is determined by using the VAST algorithm (Gibrat el al, Curr Opin Struct Bio! 6:3 ⁇ 7-385 (1996): Madej ex al , Proteins 23:356-3690 (1995)),
  • the VAST p value from a structural comparison of a ⁇ anant of the cupredoxm entry domain and P, aeruginosa azurin residues 50-77 is less than about IG "3 , less than about 10 "5 , or less than about IG 7 . in other embodiments, significant structural homology between a variant of the cupredoxin entry domain and P.
  • aeruginosa azurin residues 50-77 can be determined by using the DALl algorithm (Holm & Sander, J MoL Biol. 233:123-138 (1993)).
  • the DALI Z score for a pairwise structural comparison is at least about 3.5, at least about 7.0, or at least about 10.0.
  • cupredoxm entry domain Modifications to the cupredoxm entry domain can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis.
  • Site-directed mutagenesis Carter, Biochem J. 237: 1-7 (1986); Zoller and Smith, Methods Enzymol. 154:329-50 (1987)
  • cassette mutagenesis cassette mutagenesis
  • restriction selection mutagenesis Wells et ⁇ /., Gene 34:315-23 (1985)
  • other known techniques can be performed on the cloned DNA to produce a cupredoxin entry domain variant nucleic acid.
  • nucleotides encoding entry domains with structural similarity to that of the cupredoxin entry domains may be synthesized by methods that are well known in the art.
  • protein molecules that are wild type or variant cupredoxin entry domains may be synthesized by methods that are well known in the art.
  • the present invention provides a nucleic acid molecule encoding a fusion protein comprising a cupredoxin entry domain linked to a cargo compound, where the cargo compound is a protein or peptide.
  • the nucleic acid molecule according to the invention can be prepared by a combination of known techniques in the art. For instance. nucleic acid sequences for the cupredoxin entry domain and the cargo compound can individually be prepared by chemical synthesis or cloning. The nucleic acid sequences are then hgated in order with a Iigase to give a nucleic acid molecule of interest.
  • arginine-rich peptides are known to translocate through mammalian ceil membranes and carry protein cargo compounds mside such cells. Suzuki. T., ct al. J. Biol. Chcm. 277:2437-43 (2002).
  • a short argimne-rich 1 1 ammo acid (ammo acids 47-57) segment of HIV Tat protein allows transport of cargo proteins into mammalian cells. Schwarze, SR., et al. Trends Cell Biol. 10:290-95 (2000).
  • Synthetic entry domains that strengthen the alpha-helical content and optimize the placement of arginine residues have been shown to have enhanced potential as protein transduction domains.
  • P. aeruginosa azurin has a single arginine residue. It is therefore believed, but not relied upon for the present invention, that its mode of entry is different from that of the Tat protein.
  • the present invention encompasses the use of those cupredox ⁇ n fragments that facilitate the entry * of a cargo compound into a cell.
  • Such fragments may be determined by any method that identifies those fragments required for entry into a cell.
  • a cupredoxin fragment is linked to a marker substance and a test performed to determine whether the cupredoxin fragment enters a cell.
  • Such methods may be used to identify suitable fragments of the cupredoxins discussed above.
  • the cargo compound is attached to a cupredoxin or a fragment thereof, such as azurin from P. aeruginosa (SEQ ID NO: 1); plastocyanin from the cyanobacterium Phormidium laminosum (SEQ ID NO: 3); rusticyanin from Thiobaciilus ferrooxidans (SEQ ID NO: 4); or pseudoazurin from Achromobacter cycloclastes (SEQ ID NO: 5), a fragment of an azurin, from Pseudomonas syringae (SEQ ID XO: 21), azurin from Neisseria meningitidis (SEQ ID NO: 10), azurin from Vibrio parahaemofyticus (SEQ ID NO: 19), azurin from Bordetella bronchiseptica (SEQ ID NO: 8), auracyanin A and B from Chloroflexus aurantiacus (SEQ ID NO: 1);
  • a cupredoxin entry domain delivers a cargo compound into a ceil in vitro, ex vivo or in iivo.
  • delivery may be achieved in vitro by adding a complex of a cupredoxin entrj, domain and a cargo compound to a cell culture, such as a pap smear.
  • delivery may be achieved ex iivo by adding the complex to a sample removed from a patient, for example, blood, tissue, or bone marrow, and returning the treated sample to the patient. Delivery may also be achieved by administration of the complex directly to a patient.
  • the methods of the present invention may be used for therapeutic, prophylactic, diagnostic or research purposes.
  • Cargo compounds delivered by the present invention include, but are not limited to, proteins. lipoproteins, polypeptides, peptides, polysaccharides, nucleic acids, including anti-sense nucleic acids, dyes, microparticles or nanoparticles, toxins, organic and inorganic molecules, small molecules, and drugs.
  • a detectable substance for example, a fluorescent substance, such as green fluorescent protein; a luminescent substance; an enzyme, such as ⁇ -galactosidase; or a radiolabeled or biotinylated protein is delivered to confer a detectable phenotype to a cell.
  • a detectable substance for example, a fluorescent substance, such as green fluorescent protein; a luminescent substance; an enzyme, such as ⁇ -galactosidase; or a radiolabeled or biotinylated protein
  • microparticles or nanoparticles labeled with a detectable substance for example, a fluorescent substance
  • suitable nanoparticles is found in U.S. Pat. No. 6,383,500, issued May 7, 2002, which is hereby expressly incorporated by reference. Many such detectable substances are known to those skilled in the art.
  • the cargo compound is a detectable substance that is suitable for X-ray computed tomography, magnetic resonance imaging, ultrasound imaging or radionuclide scintigraphy.
  • the cargo compound is administered to the patient for purposes of diagnosis.
  • a contrast agent is administered as a cargo compound to enhance the image obtained by X-ray CT, MRI and ultrasound.
  • the administration of a radionuclide cargo compound that is targeted to tumor tissue via the cupredoxin entry domain can be used for radionuclide scintigraphy.
  • the cupredoxin entry domain may contain the radionucleotide with or without a cargo compound.
  • the cargo compound is a gamma ray or positron emitting radioisotope, a magnetic resonance imaging contract agent, an X-ray contrast agent, or an ultrasound contrast agent.
  • Ultrasound contrast agents suitable for use as cargo compounds include, but are not limited to, a microbubble of a biocompatible gas, a liquid carrier, and a surfactant microsphere, further comprising an optional linking moiety, U n , between the targeting moieties and the microbubble.
  • liquid carrier means aqueous solution
  • surfactant means any amphiphilic materia] which produces a reduction in interfacial tension in a solution
  • surfactant microspheres includes nanospheres, liposomes, vesicles and the like.
  • the biocompatible gas can be air, or a fluorocarbon, such as a C J -C J perfluoroalkane, which provides the difference in echogenicity and thus the contrast in ultrasound imaging.
  • the gas is encapsulated or contained in the microsphere to which is attached the cupredoxin entry domain, optionally via a linking group.
  • the attachment can be covalent, ionic or by van der Waals forces.
  • Specific examples of such contrast agents include lipid encapsulated perfluorocarbons with a plurality of tumor neovascuiature receptor binding peptides, polypeptides or peptidomimetics.
  • X-ray contrast agents suitable for use as cargo compounds include, but are not limited to, one or more X-ray absorbing or "heavy" atoms of atomic number 20 or greater, further comprising an optional linking moiety.
  • L n between the cupredoxin entry domain and the X- ray absorbing atoms.
  • the frequently used heavy atom in X-ray contrast agents is iodine.
  • X-ray contrast agents comprised of metal chelates (e.g., U.S. Pat. No. 5,417.959) and polychelates comprised of a plurality of metal ions (e.g., U.S. Pat. No. 5,679,810) have been disclosed.
  • MRI contrast agents suitable for use as cargo compounds include, but are not limited to, one or more paramagnetic metal ions, further comprising an optional linking moiety, L n , between the cupredoxin entry domain and the paramagnetic metal ions.
  • the paramagnetic metal ions are present in the form of metal complexes or metal oxide particles.
  • U.S. Pat. Nos. 5,412,148, and 5,760,191 describe examples of chelators for paramagnetic metal ions for use in MRI contrast agents.
  • U.S. Pat. No. 5,801,228, U.S. Pat. No. 5,567,41 1 , and U.S. Pat. No. 5,281,704, describe examples of polychelants useful for complexing more than one paramagnetic metal ion for use in MRI contrast agents.
  • U.S. Pat. No. 5,520,904 describes particulate compositions comprised of paramagnetic metal ions for use as MRI contrast agents.
  • a cargo compound is delivered to kill or retard cell cycle progression in a cell, such as a cancer cell.
  • a cancer cell can be, for example, an osteosarcoma cell, lung carcinoma cell, colon carcinoma cell, lymphoma cell, leukemia ceil, soft tissue sarcoma cell or breast, liver, bladder or prostate carcinoma cell.
  • the cargo compound can be a cell cycle control protein, such as p53; a cycl in-dependent kinase inhibitor, such as pi 6, p21 or p27; a suicide protein such as thymidine kinase or nitroreductase; a cytokine or other immunomodulatory protein such as interleukin 1.
  • the cargo compound is a nucleic acid.
  • the nucleic acid codes for one of the above classes of compounds.
  • the cargo compound is a drug used to treat cancer.
  • drugs include, for example. 5-fluorouracil; Interferon ⁇ ; Methotrexate; Tamoxifen; and Vincristine. The above examples are provided for illustration only, many other such compounds are known to those skilled in the art.
  • the nucleic acid is useful for gene therapy.
  • Cargo compounds suitable for treating cancer include, but not limited to. alkylating agents such as nitrogen mustards, alkyl sulfonates, nitrosoureas, ethyl enimines, and triazenes; antimetabolites such as folate antagonists, purine analogues, and pyrimidine analogues; antibiotics such as anthracyclines, bleomycins, mitomycin, dactinomycin, and plicamycin; enzymes such as L-asparaginase; farnesyl-protein transferase inhibitors; 5. alpha.
  • alkylating agents such as nitrogen mustards, alkyl sulfonates, nitrosoureas, ethyl enimines, and triazenes
  • antimetabolites such as folate antagonists, purine analogues, and pyrimidine analogues
  • antibiotics such as anthracyclines, bleomycins, mitomycin, dactino
  • -reductase inhibitors include inhibitors of 17.beta.-hydroxysteroid dehydrogenase type 3; hormonal agents such as glucocorticoids, estrogens/anti estrogens, androgens, antiandrogens, progestins, and luteinizing hormone-releasing hormone antagonists, octreotide acetate; microtubule-disruptor agents, such as ecteinascidins or their analogs and derivatives; microtubule-stabilizing agents such as taxanes, for example, paclitaxel (TaxolTM) > docetaxel (TaxotereTM), and their analogs, and epothilones, such as epothilones A-F and their analogs; plant-derived products, such as vinca alkaloids, epipodophyllotoxins, taxanes; and topiosomerase inhibitors; prenyl-protein transferase inhibitors; and miscellaneous agents such as hydroxyurea
  • anti-cancer and cytotoxic agents include but are not limited to mechlorethamine hydrochloride, cyclophosphamide, chlorambucil, melphalan, ifosfamide. busuifan, carmusti ⁇ i. lomusti ⁇ c, semustine. streptozoci ⁇ . thiotepa. dacarbazine. methotrexate, thioguanine. mercaptopurine, fludarahine, pentastatin, cladribin. eytarabine.
  • fluorouracil fluorouracil, doxorubicin hydrochloride, daunorubicin, idarubicin, bleomycin sulfate, mitomycin C, actinomycin D, safrac ⁇ ns, saframycins, quinocarcins, discodermolides. vincristine, vinblastine, vinorelbine tartrate, etoposide, etoposide phosphate, teniposide, paclitaxel. tamoxifen, estramustine, estramustme phosphate sodium, flutamide, buserelin. leuprohde. pfend ⁇ nes. diynescs, arnisole, aflacon.
  • interferon interferon, mterleukms, aldesleukin. filgrastim, sargramost ⁇ n. rituximab.
  • BCG tretinoin, irinoteean hydrochloride, betamethosone, gemcitabine hydrochloride, altretamine. and topoteca and any analogs or derivatives thereof.
  • Preferred members of these classes include, but are not limited to, paclitaxel, cisplatin, carboplatin, doxorubicin, carminomycin, daunorubiein. aminopterin. methotrexate, methopterin, mitomycin C. ecteinascidin 743. or pofiromycin, 5-fl ⁇ orouracil, 6- mercaptopurine. gemcitabine. cytosine arabinoside, podophyllotoxin or podophyllotoxin derivatives such as etoposide, etoposide phosphate or tenyposide, melphalan, vinblastine, vincristine, leurosidine, vindesine and leurosine.
  • anticancer and other cytotoxic agents useful as cargo compounds include the following: epothilone derivatives as found in German Patent No. 4138042.8; WO
  • therapeutic agents when employed as cargo compounds with the compounds of the present invention, may be used, for example, in those amounts indicated in the Physicians' Desk Reference (PDR) or as otherwise determined by one of ordinary skill in the art.
  • PDR Physicians' Desk Reference
  • compositions containing a complex of a cupredoxin entry domain linked to a cargo compound can be manufactured in any conventional manner, e.g., by conventional mixing, dissolving, granulating, dragee-making, emulsifying, encapsulating, entrapping, or lyophilizing processes.
  • the complex can be readily combined with a pharmaceutically acceptable carrier well-known in the art.
  • a pharmaceutically acceptable carrier well-known in the art.
  • Such carriers enable the preparation to be formulated as a tablet, pill, dragee, capsule, liquid, gel, syrup, slurry, suspension, and the like.
  • Suitable excipients can also include, for example, fillers and cellulose preparations.
  • Other excipients can include, for example, flavoring agents, coloring agents, detackifiers. thickeners, and other acceptable additives, adjuvants, or binders.
  • compositions can be used in, for example, the detection or imaging of a cell type or in the treatment of a condition related to cell death or in the prevention thereof.
  • the compositions can be administered in an amount sufficient to prevent or treat a condition related to resistance to cell death.
  • a condition related to resistance to cell death refers to a disease, state, or ailment characterized by at least a tendency for prolonged cell life when compared with a healthy cell of like kind as determined by a reasonable, skilled physician or clinician.
  • the host organism is a mammal, such as a human or animal.
  • compositions containing a cupredoxin entry domain can be administered by any suitable route, for example, by oral, buccal, inhalation, sublingual, rectal, vaginal, transurethral, nasal, topical, percutaneous, i.e., transdermal or parenteral (including intravenous, intramuscular, subcutaneous and intracoronary administration).
  • the compositions and pharmaceutical formulations thereof can be administered in any amount effective to achieve its intended purpose.
  • the composition is administered in a therapeutically effective amount.
  • a "therapeutically effective amount " ' is an amount effective to prevent development of. or to alleviate the existing symptoms of, the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art.
  • an indicated daily dosage for treatment in humans may be in the range from about 0.7 mg to about 1400 mg of a compound containing the cupredoxin entry domain conveniently administered, for example, in daily doses, weekly doses, monthly doses, and or continuous dosing. Daily doses can be in discrete dosages from 1 to 12 times per day.
  • doses can be administered every other day, every third day, fourth day, every fifth day, every sixth day. every week, and similarly in day increments up to 31 days.
  • Dosing can be continuous, intermittent or a single dose, using any applicable dosing form, including tablet, patches, i.v. administration and the like.
  • the composition is administered in a therapeutically effective amount.
  • the therapeutically effective amount is from about 0.01-20 rng/ " kg of body weight.
  • the dose level is about 10 mg/lcg/day, about 15 rng/kg/day, about 20 mglcg/day, about 25 mg/kg/day, about 30 mg'kg'day, about 35 mg, leg/day, about 40 mg/kg/ day, about 45 mg/kg/day or about 50 mg'kg/day.
  • the method of introducing compounds containing the cupredoxin entry domain to patients is, in some embodiments, co-administration with other drugs known to treat cancer. Such methods are well-known in the art.
  • the compounds containing the cupredoxin entry domain are part of an cocktail or co-dosing containing or with other drugs for treating cancer.
  • drugs include, for example, those listed herein and specifically 5-fluorouracil; Interferon ⁇ ; Methotrexate; Tamoxifen; and Vincristine.
  • the above examples are provided for illustration only, many other such compounds are known to those skilled in the art.
  • Nucleic acid molecules encoding a cupredoxin entry domain or a fusion protein combining a either entry domain and a cargo compound can be inserted into ⁇ ectors and used as gene therapy vectors.
  • Gene therapy ⁇ ectors can be delivered to a subject by, for example, intravenous injection, local administration (Nabel et al., U.S. Patent No. 5,328,470 1994. USA), or by stereotactic injection (Chen et ah. Proc Natl Acad Sci USA, vol.
  • the pharmaceutical preparation of a gene therap) vector cars include an acceptable diluent or can comprise a slow release main K in which the gene ss imbedded
  • the pharmaceutical preparation can include one or more cells that produce the gene delivery system.
  • the composition is delivered as DNA such that the complex is generated in situ.
  • the DNA is '"naked," as described, for example, in Ulmer ct al, Science 259:1745-49 (1993) and reviewed by Cohen, Science 259 1691-92 (1993).
  • the uptake of naked DNA may be increased by coating the DNA onto a carrier, e.g. a biodegradable bead, which is efficiently transported into the cells.
  • the DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, bacterial and viral expression systems. Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art. See, e.g., WO90/1 1092, WO93/24640, WO 93/17706, and U.S. Pat. No. 5,736,524.
  • Vectors used to shuttle genetic material from organism to organism, can be divided into two general classes: Cloning vectors are replicating plasmid or phage with regions that are non-essential for propagation in an appropriate host cell and into which foreign DNA can be inserted; the foreign DNA is replicated and propagated as if it were a component of the vector.
  • An expression vector (such as a plasmid, yeast, or animal virus genome) is used to introduce foreign genetic material into a host cell or tissue in order to transcribe and translate the foreign DNA, such as the DNA of the composition.
  • the introduced DNA is operably-linked to elements such as promoters that signal to the host cell to transcribe the inserted DNA
  • promoters are exceptionally useful, such as inducible promoters that control gene transcription in response to specific factors.
  • Operably-linking a composition polynucleotide to an inducible promoter can control the expression of the wt- azurin entry domain composition polypeptide or fragments.
  • classic inducible promoters include those that are responsive to ⁇ -interferon, heat shock, heavy metal ions, and steroids such as glucocorticoids (Kaufman, Methods Enzymol. 185:487-51 1 (1990)) and tetracycline.
  • desirable inducible promoters include those that are not endogenous to the cells in which the construct is being introduced, but. however, are responsive in those cells when the induction agent is exogenously supplied.
  • useful expression vectors are often plasm ids.
  • other forms of expression vectors such as viral vectors (e &.., replication defective retroviruses, adenoviruses and adeno-associated viruses) are contemplated.
  • Vector choice is dictated by the organism or cells being used and the desired fate of the vector.
  • vectors comprise signal sequences, origins of replication, marker genes, enhancer elements, promoters, and transcription termination sequences.
  • kits Comprising a Cupredoxin Entry Domain-Cargo Compound Complex
  • the invention provides kits containing one or more of the following in a package or container: (1) a reagent comprising a complex of a cupredoxin entry domain linked to a cargo compound; (2) a reagent containing a pharmaceutically acceptable adjuvant or excipient; (3) a vehicle for administration, such as a syringe; (4) instructions for administration.
  • a vehicle for administration such as a syringe
  • instructions for administration such as a syringe
  • compositions Comprising Cupredoxin a Cupredoxin Entry Domain, a Cupredoxin Entry Domain - Cargo Compound Complex, Or Variant, Derivative Or Structural Equivalent Thereof
  • compositions comprising cupredoxin or variant, derivative or structural equivalents thereof, can be manufactured in any conventional manner, e.g., by conventional mixing, dissolving, granulating, dragee-making, emulsifying, encapsulating, entrapping, or lyophilizing processes.
  • the substantially pure or pharmaceutical grade cupredoxin or variants, derivatives and structural equivalents thereof can be readily combined with a pharmaceutically acceptable carrier well-known in the art.
  • Such carriers enable the preparation to be formulated as a tablet, pill, dragee, capsule, liquid, gel, syrup, slurry, suspension, and the like.
  • Suitable carriers or excipierits can also include, for example, fillers and cellulose preparations.
  • compositions comprising a cupredoxin or variant, derivative or structural equivalent thereof used in the invention may be administered in a variety of ways, including by injection (e.g..
  • the composition comprising a cupredoxin or variant, derivative or structural equivalent thereof can be formulated and used directly as injectibles, for subcutaneous and intravenous injection, among others.
  • the injectable formulation in particular, can advantageously be used to treat patients that are appropriate for chemopreventive therapy.
  • the composition comprising a cupredoxin or variant, derivative or structural equivalent thereof can also be taken orally after mixing with protective agents such as polypropylene glycols or similar coating agents.
  • the cupredoxin or variant, derivative or structural equivalent thereof may be formulated in aqueous solutions, specifically in physiologically compatible buffers such as Hanks solution, Ringer's solution, or physiological saline buffer.
  • the solution may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • the cupredoxin or variant, derivative or structural equivalent thereof may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen- free water, before use.
  • the pharmaceutical composition does not comprise an adjuvant or any other substance added to enhance the immune response stimulated by the peptide.
  • the pharmaceutical composition comprises a substance that inhibits an immune response to the peptide.
  • the intravenous fluids for use administering the cupredoxin or variant, derivative or structural equivalent thereof may be composed of crystalloids or colloids.
  • Crystalloids as used herein are aqueous solutions of mineral salts or other water-soluble molecules.
  • Colloids as used herein contain larger insoluble molecules, such as gelatin.
  • Intravenous fluids may be ste ⁇ le.
  • Crystalloid fluids that may be used for intravenous administration include but are not limited to. normal saline (a solution of sodium chloride at 0.9% concentration). Ringer's lactate or Ringer's solution, and a solution of 5% dextrose in water sometimes called D5W, as described in Table 2. Table 2. Composition of Common Crystalloid Solutions
  • the cupredoxin or variant, derivative or 5 structural equivalent thereof may be delivered in the form of an aerosol spray from pressurized packs or a nebulizer with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, carbon dioxide or other suitable gas.
  • a suitable propellant e.g., dichlorodifluoromethane, trichlorofluoromethane, carbon dioxide or other suitable gas.
  • the dosage unit may be determined by providing a valve to deliver a metered amount.
  • Capsules and cartridges of, e.g., gelatin, for use in an inhaler or0 insufflator may be formulated containing a powder mix of the proteins and a suitable powder base such as lactose or starch.
  • cupredoxin or variant, derivative or structural equivalent thereof When administration is by topical administration, the cupredoxin or variant, derivative or structural equivalent thereof may be formulated as solutions, gels, ointments, creams, jellies, suspensions, and the like, as are well known in the art.
  • 5 administration is by means of a transdermal patch.
  • cupredoxin or variants and derivatives thereof compositions may also be formulated in compositions containing conventional suppository bases.
  • cupredoxin or variant, derivative or structural equivalent thereof can be readily formulated by combining the cupredoxin or variant,t) derivative or structural equivalent thereof with pharmaceutically acceptable earners vteli known in the art
  • a solid carrier such as mannitol, lactose, magnesium stearate, and the like may be employed; such carriers enable the cupredoxin and variants, derivatives or structural equivalent thereof to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a subject to be treated.
  • suitable excipients include fillers such as sugars, cellulose preparation, granulating agents, and binding agents.
  • cupredoxin or variant, derivative or structural equivalent thereof allow for the release of cupredoxin or variant, derivative or structural equivalent thereof over extended periods of time, such that without the sustained release formulation, the cupredoxin or variant, derivative or structural equivalent thereof would be cleared from a subject's system, and/or degraded by, for example, proteases and simple hydrolysis before eliciting or enhancing a therapeutic effect.
  • the half-life in the bloodstream of the peptides of the invention can be extended or optimized by several methods well known to those in the art.
  • the peptide variants of the invention may include, but are not limited to, various variants that may increase their stability, specific activity, longevity in the bloodstream, and/or decrease immunogenicity of the cupredoxin, while retaining the ability of the peptide to inhibit the development of premalignant lesions in mammalian cells, tissues and animals.
  • Such variants include, but are not limited to, those which decrease the hydrolysis of the peptide, decrease the deamidation of the peptide, decrease the oxidation, decrease the immunogenicity, increase the structural stability of the peptide or increase the size of the peptide.
  • Such peptides also include circularized peptides (see Monk ct a!,, BioDrugs 19f4):261-78, (2005); DeFreest et ah. J. Pept. Res. 63(5):409 ⁇ 19 (2004)).
  • DX-peptides diastereomeri, Futaki et a!., j, Biol. Chem. Feb 23:276(8):5836-40 (2001 ); Papo a aL Cancer Res. 64(] ⁇ ):5779 ⁇ 8 ⁇ (2004); Miller et al., Biochem, Pharmacol. 36 ⁇ l):169-76, (19S”?)); peptides containing unusual amino acids (see Lee et al., J. Pept.
  • the pharmaceutical composition includes carriers and excipients (including but not limited to buffers, carbohydrates, mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacte ⁇ ostats.
  • chelating agents suspending agents, thickening agents and/or preservatives
  • water oils, saline solutions, aqueous dextrose and glycerol solutions, other pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as buffering agents, tonicity adjusting agents, wetting agents and the like.
  • suitable carrier known to those of ordinary skill in the art may be employed to administer the compositions of this invention, the type of carrier will vary depending on the mode of administration.
  • Compounds may also be encapsulated within liposomes using well-known technology.
  • Biodegradable microspheres may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Patent Nos.
  • compositions may be sterilized by conventional, well-known sterilization techniques, or may be sterile filtered.
  • the resulting aqueous solutions may be packaged for use as is, or lyopbilized, the lyophilized preparation being combined with a sterile solution prior to administration.
  • cupredoxin or variant, derivative or structural equivalent thereof can be administered formulated as pharmaceutical compositions and administered by any suitable route, for example, by oral, buccal, inhalation, sublingual, rectal, vaginal, transurethral, nasal, topical, percutaneous, i.e., transdermal or parenteral (including intravenous, intramuscular, subcutaneous and intracoronary) or vitreous administration.
  • the pharmaceutical formulations thereof can be administered in any amount effective to achieve its intended purpose. More specifically, the composition is administered in a therapeutically effective amount. In specific embodiments, the therapeutically effective amount is generally from about 0.01 -20 mg/day/kg of body weight.
  • the compounds comprising cupredoxin or ⁇ ariant, derivathe or structural equivalent thereof are useful for the prevention of cancer, alone or in combination w. ith other active agents and ⁇ cargo compounds.
  • the appropriate dosage will, of course, vary depending upon, for example, the compound of cupredoxin or variant, derivative or structural equivalent thereof employed, the host, the mode of administration and the nature and severity of the potential cancer. However, in general, satisfactory results in humans are indicated to be obtained at daily dosages from about 0.01-20 mg/kg of body weight.
  • An indicated daily dosage in humans is in the range from about 0.7 mg to about 1400 mg of a compound of cupredoxin or variant, derivative or structural equivalent thereof conveniently administered, for example, in daily doses, weekly doses, monthly doses, and'or continuous dosing.
  • Daily doses can be in discrete dosages from 1 to 12 times per day. Alternatively, doses can be administered every other day. every third day, every fourth day, every fifth day, every sixth day, every week, and similarly in day increments up to 31 days or over. Alternatively, dosing can be continuous using patches, Lv. administration and the like.
  • the exact formulation, route of administration, and dosage is determined by the attending physician in view of the patient's condition. Dosage amount and interval can be adjusted individually to provide plasma levels of the active cupredoxin or variant, derivative or structural equivalent thereof, with or without a cargo compound, which are sufficient to maintain therapeutic effect. Generally, the desired cupredoxin or variant, derivative or structural equivalent thereof is administered in an admixture with a pharmaceutical carrier selected with regard to the intended route of administration and standard pharmaceutical practice.
  • the cupredoxin or variant, derivative or structural equivalent thereof is delivered as DNA such that the polypeptide is generated in situ.
  • the DNA is "naked.” as described, for example, in Ulmer et aL (Science 259:1745-1749 (1993)) and reviewed by Cohen (Science 259:1691-1692 (1993)).
  • the uptake of naked DNA may be increased by coating the DNA onto a carrier, e g,. biodegradable beads, which are then efficiently transported into the cells.
  • the DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, bacterial and viral expression systems. Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art.
  • Vectors used to shuttle genetic material from organism to organism, can be dhided into two general clashes' Cloning vectors are replicating plasmtd or phage with regions that are essential for propagation in an appropriate host cell and into which foreign DNA can be inserted; the foreign DNA is replicated and propagated as if it were a component of the vector.
  • An expression vector (such as a plasmid, yeast, or animal virus genome) is used to introduce foreign genetic material into a host cell or tissue in order to transcribe and translate the foreign DNA, such as the DNA of a cupredoxin.
  • the introduced DNA is operably-linked to elements such as promoters that signal to the host cell to highly transcribe the inserted DNA.
  • Some promoters are exceptionally useful, such as inducible promoters that control gene transcription in response to specific factors.
  • Operably-linking a cupredoxin and variants and derivatives thereof polynucleotide to an inducible promoter can control the expression of the cupredoxin and variants and derivatives thereof in response to specific factors.
  • classic inducible promoters include those that are responsive to ⁇ -interferon, heat shock, heavy metal ions, and steroids such as glucocorticoids (Kaufman, Methods Enzymol. 185:487-511 (1990)) and tetracycline.
  • desirable inducible promoters include those that are not endogenous to the cells in which the construct is being introduced, but, are responsive in those cells when the induction agent is exogenously supplied.
  • useful expression vectors are often plasmids.
  • other forms of expression vectors such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses) are contemplated.
  • the peptides of the present invention including in one embodiment, pi 8, may be used as a vector to selectively deliver therapeutic compounds into cancer cells or tumors.
  • Vector choice is dictated by the organism or cells being used and the desired fate of the vector.
  • vectors comprise signal sequences, origins of replication, marker genes, polylinker sites, enhancer elements, promoters, and transcription termination sequences.
  • Kits Comprising Cupredoxin, or Variant, Derivative Or Structural Equivalent Thereof
  • the invention provides regimens or kits comprising one or more of the following in a package or container: (1 ) a pharmacologically active composition comprising at least one cupredoxin or variant, derivative or structural equivalent thereof; (2) an additional chemopreventive drag, (3; apparatus to administer the biologically active composition to the patient, such as a synnge. nebulizer etc..
  • a kit When a kit is supplied, the different components of the composition may be packaged in separate containers, if appropriate, and admixed immediately before use.
  • kits can be supplied in containers of any sort such that the life of the different components are preserved and are not adsorbed or altered by the materials of the container.
  • sealed glass ampules may contain lyophilized cupredoxin and variants, derivatives and structural equivalents thereof , or buffers that have been packaged under a neutral, non-reacting gas, such as nitrogen.
  • Ampules may consist of any suitable material, such as glass, organic polymers, such as polycarbonate, polystyrene, etc., ceramic, metal or any other material typically employed to hold similar reagents.
  • suitable containers include simple bottles that may be fabricated from similar substances as ampules, and envelopes, that may comprise foil-lined interiors, such as aluminum or an alloy.
  • Other containers include test tubes, vials, flasks, bottles, syringes, or the like.
  • Containers may have a sterile access port, such as a bottle having a stopper that can be pierced by a hypodermic injection needle.
  • Other containers may have two compartments that are separated by a readily removable membrane that upon removal permits the components to be mixed. Removable membranes may be glass, plastic, rubber, etc.
  • Kits may also be supplied with instructional materials. Instructions may be printed on paper or other substrate, and/or may be supplied as an electronic-readable medium, such as a floppy disc, CD-ROM, DVD-ROM, Zip disc, videotape, audiotape, flash memory device etc. Detailed instructions may not be physically associated with the kit; instead, a user may be directed to an internet web site specified by the manufacturer or distributor of the kit, or supplied as electronic mail.
  • Cupredoxin or variant, derivative or structural equivalents thereof may be chemically modified or genetically altered to produce variants and derivatives as explained above. Such variants and derivatives may be synthesized by standard techniques. Cupredoxin entry domains mav be similarly modified.
  • allelic variants of cupredoxin changes can be introduced by mutation into cupredoxin coding sequence that incur alterations in the amino acid sequences of the encoded cupredoxin that do not significantly alter the ability of cupredoxin to inhibit the development of premalignant lesions.
  • non-essential amino acid residue is a residue that can be altered from the wild-type sequences of the cupredoxin without altering pharmacologic activity, whereas an "essential" amino acid residue is required for such pharmacologic activity.
  • ammo acid residues that are conserved among the cupredoxins are predicted to be particularly non-amenable to alteration, and thus "essential.”
  • Amino acids for which conservative substitutions that do not change the pharmacologic activity of the polypeptide can be made are well known in the art.
  • Non-conservative substitutions that affect (1) the structure of the polypeptide backbone, such as a ⁇ sheet or ⁇ -helical conformation, (2) the charge, (3) hydrophobicity, or (4) the bulk of the side chain of the target site can modify the pharmacologic activity.
  • Residues are divided into groups based on common side-chain properties as denoted in Table 4.
  • Non-conservative substitutions entail exchanging a member of one of these classes for another class. Substitutions may be introduced into conservative substitution sites or more specifically into non-conserved sites.
  • the variant polypeptides can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis.
  • Site-directed mutagenesis Carter, Biochem J. 237:1-7 (1986): Zollcr and Smith, Methods Enzymol. 154:329-350 (1987)
  • cassette mutagenesis cassette mutagenesis
  • restriction selection mutagenesis Wells ei aL, Gene 34:315-323 (1985)
  • other known techniques can be performed on the cloned DNA to produce the cupredoxin variant DNA.
  • cupredoxins can also be used to create variant cupredoxin to be used in the methods of the invention.
  • the Cl 12D and M44KM64E mutants of ayutm are known to have cytotoxic and growth arresting activity that is different from the native azurin. and such altered activity can be useful in the treatment methods of the present invention.
  • the mouse mammalary gland organ culture (MMOC) model allows evaluating efficacy of potentially chemopreventive agents against development of mammary alveolar lesions (MAL) or mammary ductal lesions (MDL) in response to DMBA.
  • MAL mammary alveolar lesions
  • MDL mammary ductal lesions
  • DMBA under appropriate incubation conditions form either MAL or MDL based on the hormonal milieu in the medium.
  • Estrogen and progesterone-treated glands in culture develop ductal lesions whereas aldosterone and hydrocortisone- treated glands form estrogen and progesterone-independent alveolar lesions.
  • Mammary glands not exposed to a carcinogen or chemopreventive agent undergo structural regression in the absence of growth- promoting hormones, whereas treatment with DMBA for the 24-hr period between days 3 and 4 the regression of structures caused by deprivation of hormones. It is assumed that this is because the glands have lost normal hormonal responsiveness and now have altered their course of development. Generating mammary adenocarcinoma by transplanting transformed cells into syngeneic mice has proved the prernalignant preneoplastic nature of these unrepressed areas.
  • the thoracic pair of mammary glands was excised asepticaily from each BaJb-'c mouse, and the glands were divided into several groups. The effects of p2H were evaluated at 4 different dilutions in the medium. Carcinogen treated glands without the test agent served as a measure to determine percent incidence in the absence of a chemopreventive agent. An additional control was included to serve as a positive control for chemoprevention. Azurin was included in the medium at 50 ⁇ g/ml concentration. For alveolar lesions (MAL) stained glands were evaluated for the incidence of lesions (glands containing any lesions as compared to total number of glands in a given treatment group).
  • MAL alveolar lesions
  • ductal lesions For the ductal lesions (MDL) similar protocol was adapted, however, as indicated below in the methods section the hormonal combination is different for alveolar and ductal lesions.
  • the glands were fixed in formalin and then processed for histopathology.
  • the sections are stained with eosin and hematoxelene and evaluated under microscope. Here the multiplicity of ductal lesions between the control and the treatment groups are compared.
  • mice Organ Culture Procedure.
  • the experimental animals used for the studies were young, virgin BALB/ c female mice 3 to 4 weeks of age obtained from Charles River, Wilmington, MA.
  • the mice were treated daily by subcutaneous injections with 1 ⁇ g estradiol- 17 ⁇ + 1 mg progesterone for 9 days. This treatment is a prerequisite inasmuch as animals not pretreated with steroids fail to respond to hormones in vitro.
  • the entire culture procedure is described in detail. Jang et al, Science 275:218-220 (1997); Mehta, Eu. J. Cancer 36:1275-1282 (2000); Mehta et al, J. Natl. Cancer Inst. 89:212-219 (1997); Mehta et aL, J. Natl.
  • the medium For induction of ductal lesions (MDL), the medium contained 5 ⁇ g,ml, 5 ⁇ g/ml P. 0.001 ⁇ g/ml estradiol !7 ⁇ and 1 ⁇ g/ml progesterone (Pg). Mehta et a!., J. Natl. Cancer Inst. 93:1 103-1 106 (2001).
  • the carcinogen, DMBA (2 ⁇ gml) was added to the medium between days 3 and 4.
  • DMBA was dissolved in DMSO at a final concentration of 4 nig/ml, and 50 ⁇ g I was added to 100 ml medium resulting in 2 ⁇ g/ml final concentrations.
  • the control dishes contained DMSO ⁇ S vehicle.
  • DMBA is removed from the medium by rinsing the glands in fresh medium and transferring them to new dishes containing fresh medium without DMBA. After 10 days of incubation, the glands were maintained for another 14 days in the medium containing only
  • the glands were maintained at 37°C under 95% Cb and 5% CO 2 environment.
  • the chemopreventive agent was included in the medium during the first ten days of growth -promoting phase.
  • the test peptide p28 was evaluated at 4 concentrations ranging from 12.5 ⁇ g/ml to 100 ⁇ g/ml.
  • Azurin was evaluated at 50 ⁇ gm! in the medium.
  • the peptide was dissolved in sterile water and filtered prior to use. The medium was changed three times per week (Monday, Wednesday and Friday). At the end of the exposure, the glands were fixed in formalin.
  • results were analyzed by Chi-square analysis and Fisher's Exact Test. Morphometic Analysis of MAL.
  • MAL For examination of MAL, the glands were stained in alum carmine, and evaluated for the presence of the lesions. The glands were scored for the presence or absence of mammary lesions, severity of lesions per gland, and toxicity of the agent. The glands stored in xylene were evaluated for the presence or absence, incidence, and severity of mammary lesions for each gland under a dissecting microscope. Mammary glands were scored as positive or negative for mammary lesions, and the percent incidence was determined as a ratio of glands exhibiting lesions and the total number of glands in that group. Dilation of ducts or disintegration of mammary structure because of treatment with chemopreventive agent was considered a toxic effect. The data were subjected to statistical analysis for the incidence to determine the effectiveness of the potential chemopreventive agents.
  • Figure IA shows a representative photograph of alveolar lesions in a DMBA treated gland and its comparison with a gland that was treated with DMBA along with a chemopreventive agent.
  • the effects of p28 on the development of alveolar lesion are shown in Figures I B- IF and summarized in Figure 2.
  • the peptide p28 inhibited MAL formation by 6?% at 25 ⁇ g/'ml concentration. Increasing concentration further up to 100 ⁇ g/ml did not enhance the efficacy of the peptide.
  • the comparison of the peptide with azurin indicated that p28 was as effective as azurin for MAL development. Azurin at 50 ⁇ g/ml concentration resulted in a 67% inhibition.
  • each gland will have variable number of fields. Often the number of sections through the ducts also varies greatly from gland to gland. This results in the variable number from group to group. Fields containing ductal hyperplasia or atypia were determined and were compared with total number of field evaluated for each gland. No discrimination is made between the hyperplasia or atypia and severely occluded glands. Any field containing any of these histological patterns was considered positive for the lesion. The treatment groups were compared with the controls for the severity and percent inhibition was calculated.
  • Figure 3 shows a representative ductal lesion.
  • DMBA induces ductal lesions varying from hyperplasia, atypia to complete occlusion of the ducts.
  • a ratio of ductal lesions/total number of ductal sections was determined. Again, 12.5 ⁇ g/ml concentration of p28 suppressed only 15% of the MDL formation. However, at 25 ⁇ g/ml there was a significant inhibition of the lesions comparable to that observed with 50 ⁇ g/ml azurin.
  • the efficacy of p28 at concentrations greater than 12.5 ⁇ g/ml was statistically significant (p ⁇ 0.01, Fishers Exact Test).
  • chemopreventive agents can be differentiated between the MAL and MDL. For example tamoxifen inhibited the development of MDL but not MAL, It is interesting to note that azurin and p28 inhibited both estrogen and progesterone-dependent ductal lesions as well as independent alveolar lesions. This example indicates that both p28 and azurin can pre ⁇ cm the development of precancerous lesions m breast tissue. Thus, p28 and azunrt may be used as chemopreventive agents in mammalian patients.
  • 25 amino acid (a. a.) fragments of azurin (azu) were synthesized and evaluated for their penetration into a variety of cancer and histological)' matched normal cells.
  • Confocal microscopic and flow cytometric (FACS) analysis demonstrated that an 18 amino acid (1.7kDa, azu 50-67) fragment (pi 8) labeled with Alexaftuor 568 (800Da) selecthely penetrated human melanoma (MeI-2,7,29), breast (MCF-7), ovarian (SK-OV3).
  • LDH release and hemolysis assays showed that pi 8 did not disrupt cancer cell membrane structure during penetration or produce hemolysis of human erthrocytes, suggesting that p 18 penetrates human cancer cells without disrupting membrane structure.
  • pi 8 appear to have significant utilization as a non-viral vector for gene (or an ⁇ DIs A'RNA fragment) therapy.
  • Figure 5 shows a schematic representation of ⁇ a ⁇ ous truncated wt-a/urin constructs For pGST-aru 36-12H (SEQ ID NO' 34), ⁇ ui amplified PCR fragment wax introduced into the BamHl and EcoRl sites of the commercial GST expression vector pGEXSX (Arnersham Bioseiences, Piscataway, NJ 08855).
  • the fragment was amplified with pUC19-azu as a template and primers, 5'-CGGGATCC CCG GCA ACC TGC CGA AGA ACG TCA TGG GC-3 " (SEQ ID NO: 35) and 5'-CGGAATTC GCA TCA CTT CAG GGT CAG GG-3' (SEQ ID NO: 36). where the additionally introduced BamHl and EcoRI sites are underlined respectively.
  • Carboxyl-terminus truncation oiazu gene was cumulatively performed by introducing a stop codon using QuickChange site-direct mutagenesis kit (Stratagene. La Jolla, CA 92037).
  • pGST-azu 36- ⁇ 7 (SEQ ID NO: 38) and pGST- azu 36-89 (SEQ ID NO: 39) stop codons were introduced into Ser51, Ser78. and Gly90, respectively.
  • the plasmid carrying pGST-azu 36-128 was used as template DNA.
  • Three sets of oligonuclotides for site-direct mutagenesis are shown as follows.
  • Amplified PCR fragments azu 50-77 and azu 67-77, were obtained using forward primers 5'-CGGGATCC TGA GCA CCG CCG CCG ACA TGC AGG G-3' (SEQ ID NO: 46) and 5'-CGGGATCC CCG GCC TGG ACA AGG ATT ACC TGA AGC CCG-3 (SEQ ID NO: 47), where the additionally introduced BamHl site is indicated by underlining.
  • the plasmid carrying gst-azu 50-7" was used for generating pGST-azu 50-66 by introduction of a stop codon in GIy67 using oligonuclotides as follows: 5'-GAC GGC ATG GCT TCC TGA CTG GAC AAG GAT TAC C -3 " (SEQ ID NO: 49), and 5 ! -GGT AAT CCT TGT CCA GTC AGG AAG CCA TGC CGTC- 3' (SEQ ID NO: 50),
  • the green fluorescent protein gene ⁇ gfp ⁇ encoding the green fluorescent protein was also amplified by PCR.
  • Forward and reverse primers used were 5'-CGGGATCC CCA TGG TGA GCA AGGGCG-3' (SEQ ID NO: 51) and 5'-CGGAATTC CTT GTA CAG CTC GTC CAT GCC G-3' (SEQ ID NO: 52) containing BamHl and EcoRl sites at the 5 5 end of each oligomiclotides.
  • the resultant PCR fragment was ligated into the pGEXSX vector for creating pGST-GFP.
  • the azu 50-77 geoe was amplified by PCR with pGST-a/u 50-77 as a template and primers 5' - CCGCTCGAG CCT GAG CAC CGC CGC CATGCA GGG-3' (SEQ ID NO: 53) and 5' - TTTTCCTTTTGCGGCCGC TCA GTC GTC GGG CTT CAG GTA ATC C-3 " (SEQ ID NO: 54), where the introduced Xho I and .Vo/ 1 sites are underlined respectively. Purified azu 50-77 fragment was introduced into pGST-GFP at Xlio 1 and Not 1 unique restriction enzyme sites
  • Wt-azurin and M44KM64E mutant azurin were prepared and purified as described by Yamada, T. et al. Proc. Natl. Acad, Sci. USA, vol. 1 OL pp. 4770-75 (2004), and in copending U.S. patent application serial number 10/720,603, the contents of which are incorporated by this reference. Briefly, the wt-azurin gene was amplified by PCR according to the method described by Kukimoto et ah, FEBS Lett, vol. 394, pp 87-90 (1996). PCR was performed using genomic DNA from P. aeruginosa strain PAOl as a template DNA.
  • E. col JM 109 was used as a host strain for expression of the azurin gene.
  • the recombinant E, coil strain was cultivated in 2YT medium containing 50 ⁇ g ml ampicillln, 0.1 m ⁇ l IPTG: and 0.5 mM CUSO ⁇ for 16 h at 37°C to produce azurin.
  • site-directed mutagenesis of the azurin gene was performed using a QuickChange site-directed mutagenesis kit (Stratagene. La Jolla, CA). Mutations were confirmed by DNA sequencing.
  • GST- fusion proteins were purified from cell extracts by using Glutathione Sepharose 4B affinity chromatography and Sephadex 75 gel- filtration column with PBS (Amersham Biosciences, Piscataway, NJ 08855). Purified proteins, wt azurin and GST- derivatives or other cupredoxins, labeled with ALEXA FLUOR* (Molecular Probes, Inc., Eugene, OR 97402) were isolated according to manufacturer's instructions. Unbound free fluorescent chemical was removed by gel-filtration column.
  • Example 5 Cell cultures J774 and UISO-Mel-2 cells (available from Frederick Cancer Research and
  • Human normal fibroblast cells (stock culture collection of the Department of Surgical Oncology, University of Illinois at Chicago (UIC), Chicago) were cultured in MEM with Eagle ' s salt containing 2 mM L- glutamine, 0.1 mM MEM essential amino acids and supplemented with 10% heat inactivated fetal bovine serum, 100 Units/ml penicillin and 100 ⁇ g/m! streptomycin.
  • MCF- 7 and MGF- 1OF cells were cultured as described in Punj et al. Oncogene 23:2367-78 (2004).
  • Example 6 Co-culture of J774, UISO- ⁇ lei-2 and Fibroblast Cells and Confocal microscopy
  • J774, UISO-Mel-2, and fibroblast cells were cultured on individual cover slips. After overnight incubation, the cells were washed with fresh media and all three cell lines were placed on a culture dish containing 200 ⁇ g'ml of wt-azurin conjugated with ALEXA 1 FLUOR* 568. The cells were then incubated for 0.5 or 3.5 h at 37 0 C under 5% CO 2 .
  • cells were cultured on cover-slips overnight at 37 y C. Cultured cells were placed at 37 ⁇ C or 4 0 C for 2 h before protein treatment. Pre- warmed 37 ⁇ C fresh media or ice-cold 4 ⁇ C fresh media were mixed with red- fluorescent (labeled with ALEXA FLUOR ⁇ 568) cupredoxins or GST- fusion derivatives, and incubated with the cells. The cells were washed with PBS, and fixed with methanol at -2O 0 C for 5 min.
  • Example 7 Entry of Cupredoxins into J774 Cells Wt-azurin, its mutant variant M44KM64E, piastocyanin, pseudoazurin and rusticyanin were incubated with J774 cells as in Example 6 and the cells examined using confocal microscopy.
  • the cupredoxins were conjugated with ALEXA FLUOR ® 568 to fluoresce red and incubated with the J774 cells for 1 hr at 37 0 C at a concentration of 200 ⁇ g/ml, and in a separate experiment wild type azurin and rusticyanin were incubated with J774 cells for 1 hr at 37°C at a concentration of about 6 to 7 ⁇ M.
  • the nucleus was stained blue with DAPL A control without the proteins was maintained. In all cases, the cupredoxins were seen to enter into the cytosol of J774 cells. In similar experiments, auracyanin A and B enter preferentially to MCF7 cancer cells and not noncancerous control cells.
  • Wt-azurin exhibits a reduced cytotoxic activity towards MCF-IOF cells as contrasted with the MCF-7 cells. Punj ct al Oncogene 23:2367-2378 (2004). J774. peritoneal macrophages, mast cells, human breast cancer MCF- 7 and human normal epithelial VfCF- I OF cells (stock culture collection of the Department of Surgical Oncology, University of Illinois at Chicago (UIC), Chicago) were treated and examined as in Example 5 and tested to determine if wt-azurin could enter such cells.
  • Wt-azu ⁇ n was internalized in J774 cells during 45 mm incubation. However, it was internalized very inefficiently in peritoneal macrophages or mast cells. Even after 6 hr incubation, such cells showed only limited entry. Similarly, while wt-azurin entered the breast cancer MCF-? cells efficiently, it showed an extremely reduced rate of entry in the normal mammary MCF-IOF cells.
  • Alexa fluor ⁇ -conjugated azurin entered efficiently in UISOMel-2 and MCF-7 cancer cells but not in the normal mammary MCF 10Al cells.
  • Alexa fluor* -conjugated rusticyanin not only entered the cytosol of UISO-Mel-2 and MCF-7 cancer cells, but also in the normal MCF 10Al cells.
  • M44KM64E mutant azu ⁇ n showed very little apoptos ⁇ s -inducing activity in J774 cells but at 1 mg,ml concentration significantly inhibited (about 95%; cell cycle progression at the G ? to S phase. Ceil progression was analyzed by flow cytometry, as described by Hiraoka. Y. et al .. Proc Nad Acad. Sc USA, 101 6427-32 (2004) and Yamada, T. ct al Proc Natl Acad. ScL USA 101:4770-75 (2004), the contents of which are incorporated by reference.
  • Figure I (a) shows that when the fibroblasts were treated with 500 ⁇ g.ml or I mg ml of M44KM64E mutant azurin, the extent of inhibition of cell cycle progression was about 20%.
  • Example 10 Microinjection of Wt-azurin into Fibroblast and MCF-IOF ceils Wt-azurin was microinjected into fibroblast and MCF-IOF cells as using the method described by Punj. V., et aL, Oncogene 23:2367-78 (2004). Cells were examined for induction of apoptosis, leading to nuclear DNA condensation and fragmentation. Significant nuclear DNA (labeled blue with DAPI) condensation and fragmentation were observed in microinjected single cells after 5 hr incubation with wt-azurin, but not during a 30 min. incubation with azurin.
  • DAPI nuclear DNA
  • Example 11 Internalization of Wt-azurin Fusion Derivatives at 37°C
  • a series of GST fusions of wt-azurin truncated at both the N- and the C-terminal were prepared and purified as in Example 1 ( Figure 2(a) and 2(b)).
  • ALEXA FLUOR* 568 conjugated wt-azurin GST and GST-azu fusion derivatives
  • internalization in J774 cells at 37 0 C during 1 hr incubation was examined using the method desc ⁇ bed in Example 5. The nucleus was stained blue with DAPL While wt-azurin was internalized, GST remained at the periphery of the cells and was not internalized.
  • GST-azu 36-128 and GST-azu 36-89 were internalized, as was GST-azu 36- 77. Further truncations, however, demonstrated that while GST-azu 50-77 was internalized, GST-azu 36-50 was highly inefficient and appeared to form clumps on the surface.
  • GST was fused with GFP to make a GST-GFP fusion derivative. Additionally, azu 50-77 was fused to the GST-GFP (M r 53 kDa) fusion protein ( Figure 6(a)). The mobility of the purified GST, GST-GFP and GST-GFP-azu 5G- 7 7 fusion derivatives was examined on SDS-PAGE ( Figure 6(b)). Detection was by Coomassie Blue staining and Western blotting using anti-azurin antibody ( Figure ⁇ (c))
  • GST-GFP and GST-GFP-azu 50-77 both J774 and UISO-Mel-2 cells were incubated with GST-GFP and GST-GFP-azu 50-77 at 37 0 C and at 4°C. The green fluorescence was localized using confocal microscopy.
  • GST-GFP fusion protein bound to the surface and was not internalized both at 37 0 C and at 4°C.
  • GST-GFP-azu 50-77 was found to be internalized at 37°C, but not at 4°C.
  • LTSO-Mel-2 cells the GST-GFP fusion protein was retained on the surface both at 37 0 C and at 4°C.
  • GST-GFP-azu 50-77 fusion protein was seen to be internalized at 37 0 C but not at 4 0 C.
  • wt-azurin entry is solely dependent on receptor-mediated endocytosis, it could be blocked by protonophore carbonyl cyanide m-chlorophrnylhydrazone (CCCP), a mitochondrial uncoupler of energy generation, or preincubalion with unlabeled azurin or other cupredoxins that block the receptors, J774 and UISO-MeI- 2 cells were incubated with the eupredoxins at 10 fold excess concentration for 2 hr at 4 3 C, the cells washed thoroughly to remove the eupredoxins. and incubated with ALEXA FLUOR* 568-conjugated azurin for 1 hr at 37°C.
  • CCCP protonophore carbonyl cyanide m-chlorophrnylhydrazone
  • cytochalasin D available from Sigma- Aldrieh, St, Louis, Mo 63195
  • Brefeldin A available from Sigma- Aldrich, St. Louis, Mo 63195
  • CCCP at 20 pM concentration significantly reduced the uptake of azurin in UISOMeI-2 cells as did 0.25 to 0.5 pM cytoehalasin D.
  • Brefeldin A had no significant effect.
  • PEDlII Pseudomonas aeruginosa exotoxin A domain III
  • A54PT61PK70P mutant azurin was prepared by site-directed mutagenesis of the azurin gene using the QuickChange site-directed mutagenesis kit (Stratagene, La Jolla. CA).
  • the mutants were incubated at 200 ⁇ g/ml with UISO-Mel-2 cells for 1 hr at 37°C, after which the fluorescence was localized by confocal microscopy.
  • the ALEXA FLUOR* 568-conjugated mutant azurins entered UISO-Mel-2 cells.
  • the GST-GFP-azu 50-77 fusion protein, as weli as its triple A54PT61PK70P azu mutant variant were examined for entry in UISO-Mel-2 cells, no significant difference was observed.
  • a GST- fusion of Pseudomonas aeruginosa exotoxin A domain III was constructed as in Example 15.
  • PEDIH Pseudomonas aeruginosa exotoxin A domain III
  • Example 15 A GST-fusion of Pseudomonas aeruginosa exotoxin A domain III (PEDIH) and was constructed as in Example 15.
  • full- length rusticyanin sequence was introduced to the carboxyl end of the GST-PEDIII fusion protein.
  • the fusion protein was purified by glutathione-sepharose 4B column chromatography.
  • UISO-Mel-2 and FBT cells were then incubated for 24 h at 37°C with various concentrations of the fusion protein and the extent of cell death measured by MTT assays as described in Example 7.
  • the GST-PEDIII- rusticyanin fusion protein exhibited high cytotoxicity against UISO-Mel-2 ceils ( Figure 9). In contrast, the fusion protein demonstrated only a low level of cytotoxicity towards the FBT cells.

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Abstract

The present invention discloses methods and materials for delivering a cargo compound into a cancer cell. Delivery of the cargo compound is accomplished by the use of protein transduction domains derived from cupredoxins. The cargo compound may be a nucleic acid and specifically a DNA, RNA or anti-sense. The invention further discloses methods for treating cancer and diagnosing cancer.

Description

COMPOSITIONS AND METHODS TO PREVENT CANCER WITH
CLPREDOXINS
RELATED APPLICATIONS
This application claims priority under 35 U.S. C. §§ 1 19 and 120 to U.S. Patent
Application Seπal No. 1 1 '488,693, filed July 19, 2006, U.S. Patent Application Serial Xo.
60' 844.358, filed September 14. 2006, which claims priority to U.S. Patent Application No.
1 L 244.105, filed October 6, 2005, which claims priority to U.S. Provisional Patent Application Serial No. 60/616.782, filed October 7, 2004, and U.S. Provisional Patent
Application Serial No. 60'680,5GO, filed May 13- 2005, and is a continuation-in-part of U.S.
Patent Application Serial Number 10/720,603, filed November 1 1 , 2003, which claims priority to U.S. Provisional Patent Application Serial No. 60/414.550. filed August 15, 2003. and which is a continuation-in-part of U.S. Patent Application Seπal Number 10 047,710, filed January 15, 2002, which claims priority to U.S. Provisional Patent Application Serial
Number 60/269,133, filed February 15, 2001.
STATEMENT OF GOVERNMENTAL INTEREST The entire content of these prior applications is fully incorporated herein by reference.
The subject matter of this application has been supported by research grants from the National Institutes of Health (NlH), Bethesda, iMaryland, U.S.A.. (Grant Numbers AI 16790-
21, ES 04050-16, AI 45441, CA09432 and N01-CM97S67. The government may have certain rights in this invention.
FIELD OF THE INVENTION The present invention relates to compositions comprising variants, derivatives and structural equivalents of cupredoxins that inhibit the development of premalignant lesions in mammalian ceils, tissues and animals. The invention also relates to the use of cupredoxins. and variants, derivatives and structurally equivalents of cupredoxins, as chemopre\ entive agents in mammals to inhibit the development of premalignant lesions, and ultimately cancer.
4. BACKGROUND
Cancer chemoprevention is the use of natural, synthetic or biologic chemical agents to reverse, suppress, or prevent carcinogenic progression to invasive cancer. Recent clinical trials in preventing cancer in high-risk populations suggest that chemopreventive therapy is a realistic treatment for high-risk patients. Chemopreventive therapy is based on the concepts of multifocal field carcinogenesis and multistep carcinogenesis. In field carcinogenesis, generalized carcinogen exposure throughout the tissue field results in diffuse epithelial injury in tissue and clonal proliferation of the mutated cells. These genetic mutations throughout the field increase the likelihood that one or more premalignant or malignant lesions may develop in the field. Multistep carcinogenesis in the stepwise accumulation of these genetic and phenotypic alterations. Arresting one or more steps in the multistep cancinogenesis may impede or prevent the development of cancer. See generally Tsao ct ah, CA Cancer J Clin 54: 150-180 (2004). Azurin, and other cupredoxins. are cytotoxic specifically towards cancer cells. Azurin induces apoptosis in J774 lung cancer cells. Yamada et ah, PNAS 99(22): 14098-14103 (2002). On entry into J774 lung cancer cells, azurin localizes in the cytosol and nuclear fractions, and forms a complex with tumor suppressor protein p53, thereby stabilizing it and enhancing its intracellular level. Id. The induction of azurin-mediated apoptosis is not limited to J774 cells. Azurin can also enter cancer cells such as human melanoma UISO- MeI -2 or human breast cancer MCF-7 cells. Yamada ct ai, Infect ϊnimun. 70:7054-7062 (2002); Punj et ah, Oncogene. 23:2367-2378 (2004). In both cases, azurin allowed the elevation of the intracellular p53 levels, leading to enhanced Bax formation and induction of apoptosis in such cells. Most interestingly, intraperitoneal injection of azurin in nude mice harboring xenografted Mel-2 or MCF-7 human cancers led to statistically significant regression of such cancers. Id.
The mouse mammary gland organ culture (MMOC) assay may be used to evaluate the inhibitory effects of potential chemopreventive agents on both hormone-induced structural differentiation of mammary glands and on the development of DMBA-induced preneoplastic hyperplastic alveolar nodule-like lesions in the gland. Mammary glands from young, virgin animals. 1A hen incubated for 6 days in the presence of msulin (I) ÷ prolactin (P) - aldosterone (Aj, can differentiate into tully-grown glands These glands morphologically resemble the
.?_ glands obtained from pregnant mice. Aldosterone can be replaced by estrogen (E) -*■ progesterone (Pg) Inclusion of hydrocortisone (H) to the medium stimulates the functional differentiation of the mammary glands. Mehta and Banerjee, Acta Endocrinol. 80:501 (1975); Mehta and Moon. Breast Cancer-: Treatment and Prognosis 300, 300 (Basil A Stoll ed.. Blackweil Press 1986). Thus, the hormone-induced structural and functional differentiation, observed in this culture system, mimics the responses to hormones observed during various physiological stages of the animal.
Mice exhibit a distinct preneoplastic stage prior to cancer formation in MMOC. Such preneoplastic lesions in C3H mice are induced by murine mammary tumor virus or in BALB'c mice by DMBA. Exposure of the glands to 2 μg/ml DMBA between days 3 and 4 of growth phases followed by regression of the glands for 2-3 weeks in the medium containing only insulin, results in the formation of mammary alveolar lesions (MAL). Hawthorne et al., Pharmaceutical Biology 40:70-74 (2002); Mehta et al., Methods in Cell Science 19:19-24 (1997). Furthermore, transplantation of epithelial cells, prepared from glands containing the DMBA-induced mammary lesions, into syngeneic host resulted in the development of mammary adenocarcinoma. Telang et al., PNAS 76:5886-5890 (1979). Pathologically, these tumors were similar to those observed in vivo when mice of the same strain are administered DMBA. Id.
DMBA-induced mammary lesion formation in MMOC can be inhibited by a variety of classes of chemopreventive agents such as retinoids. These agents include chemopreventive agents derived from the natural products such as brassinin and resveretrol, thiols, antioxidants, inhibitors of ornithine decarboxylase such as OFMO and deguelin, inhibitors of prostaglandin synthesis, Ca regulators, etc., Jang et al., Science 275:218-220 (1997); Mehta, Eur. J. Cancer 36:1275-1282 (2000); Metha et al., J. Natl. Cancer Inst. 89:212-219 (1997). These studies clearly demonstrate that this organ culture system offers a unique model to determine the effectiveness of compounds against mammary carcinogenesis. The results can be expected to closely correlate to the inhibition obtained by in vivo administration of such compounds.
The MMOC may also be induced to form mammary ductal lesions (MDL). The MDL can be induced if estrogen and progesterone instead of aldosterone and hydrocortisone are included in the medium The alveolar structures in the presence of ovarian steroids are very small but the intraductal lesions are observed in histupatholυgica! sections. Mehta ei al, J Natl. Cancer Inst. 93: 1 103-1 106 (2001). The antiestrogens, which selectively work on ovarian hormone dependent ER+ breast cancers such as tamoxifen, inhibited MDL formation and not MAL. Thus, this modified culture model in addition to conventional MAL induction protocol now can be used to evaluate effects of chemopreventive agents on both MAL and MOL.
What is needed is a chemopreventive agent that inhibit the development of premalignant lesions. Such a chemopreventive agent should be able to either prevent the initial development of premalignant lesions, induce cell death m premalignant lesions that form, and/or prevent the development of premalignant lesions into malignant lesions. Such chemopreventive agents would have great utility in treating, in particular, patients who are at a high risk of developing cancer, due to either the presence of high-risk features, the presence of pre-malignant lesions, or the previous of cancer or premalignant lesions.
The entry of a protein into a mammalian cell is often dictated by a small segment of the protein, which is commonly referred to as a "protein transduction domain" or PTD. This segment can be used as a signal attached to a foreign protein to facilitate transport of such a protein into a mammalian cell. For example, amphipathic peptides are used to facilitate uptake of DNA-cleaving metalloporphyrins as potential antitumor drugs in human fibroblasts HS68 or murine lymphocytic leukemia L1210 cells (Chaloin, L. et al. Bioconjugate Chem. 12:691-700, (2001)). Peptides, called cell-penetrating peptides, such as penetratin, transportan, Tat (amino acids 47-57 or 48-60) and the model amphipathic peptide MAP, have been used as delivery vehicles for transporting pharmacologically important substances, such as antisense oligonuclotides, proteins and peptides (Hallbrink, M. et al. Biochim. Biophys. Acta 1515:101-109 (2001); Lindgren. M., et al Trends Pharmacol. Sci. 21 :99-103 (2000)). Such peptides, particularly the DNA-binding homeodomain of Λntennapedia, a Drosophila transcription factor, or the 21 residue peptide carrier Pep-1, are internalized by many types of cells in culture, such as human HS6S or murine NΪH-3T3 fibroblasts, at either 370C or 40C. The lack of effect of the temperature shift suggests a penetration mechanism different from that of classical endocytosis (Morris. M. C. et al Nature Biotechnol. 19:1173- 1176 (2001)), which requires chiral receptor proteins. One of the most widely used peptides to transport pharmacologically-active compounds in mammalian cells is the eleven amino acid argϊrsine-rich protein transduction domain (PTD) of the human immunodeficiency virus type I fHϊV-l ) transactϊvator protein Tat (Seimarze, S. R, a al Science 285:1569-1572 (1999), Schwarze, S.R. et al Trends Cell Biol. 10:290-295 (2000)). Intraperitoneal injection of the 120 kDa beta-gal actosidaso Tat fusion protein results in the transceliuiar transduction of the fusion protein into virtually all tissues in mice, including the passage of the blood-bram barrier. This short peptide domain of HIV-I Tat has been shown to mediate cell internalization of large molecules or particles, including magnetic nanopartieles, phage vectors, liposomes and plasmid DNA. Unlike the other cell-penetrating peptides discussed above, internalization of cargo proteins by full length Tat or its 11 amino acid transduction domain is significantly impaired at 40C (Uu. Y. et al Nat. Med. 6: 1380-1387 (2000). Suzuki, T. et al J. Biol. Chem. 277:2437-2443 (2002)) and requires interactions with receptors such as the heparan sulfate chains of the cell membrane heparan sulfate proteoglycans.
Most of the PTDs identified to date have been derived from viral and mammalian sources. Other sources of PTDs would be desirable for the design of various experimental sequences, and for animal and human therapies and prophylactic procedures. One alternative source of PTDs is bacterial cells. Although bacterial proteins such as cholera toxin are known to enter mammalian cell cytosol (Sofer, A. and Futerman, A.H. J. Biol. Chem.
270: 12117-12122 (1995)), the cytotoxicity of such proteins has limited the use of bacterial proteins, or PTDs derived from them, for transporting pharmacologically important cargos in mammalian cells.
SUMMARY OF THE EMBODIMENTS
The present invention relates to compositions comprising peptides that may be variants, derivatives and structural equivalents of cupredoxins that inhibit the development of premalignant lesions in mammalian cells, tissues and animals. Specifically, these compositions may comprise azurin from Pseudomonas aeruginosa, the 50-77 residue region of azurin (p28) SEQ ID NO: 2, and the 50-67 residue region of a/urin (ptS) SEQ ID NO: 25 The present invention further relates to compositions that may comprise cupredoxin(s), and/or variants, derivatives or structural equivalents of cupredoxins, that retain the ability to inhibit the development of premalignant lesions in mammalian cells, tissues or animals. These compositions may be isolated peptides or pharmaceutical compositions, among others. The compositions of the invention may be used in methods to prevent the development of cancer in mammalian patients. One aspect of the invention are isolated peptides that may be a variant, derivative or structural equivalent of a cupredoxin; and may inhibit the development of premalignant lesions in mammalian tissue. The cupredoxin may be azurin, pseudoazurin, plastocyanin, ruslicyanin. Laz, auracyanin, stellacyanin and cucumber basic protein, and specifically may be azurin. The cupredoxin may be from an organism such as Pseudomonas aeruginosa.
Λlcaligenes faecalis, Uha pertussis, Achromobacter xylosoxidan, Bordetella bronchiseptica, Methylomonas sp., Neisseria meningitidis, Neisseria gonorrhea* Pseudomonas fluorescens, Pseudomonas chlororaphis , Xyiella fastidiosa and Vibrio parahaemolyiicus, and specifically may be Pseudomonas aeruginosa. In some embodiments, the peptide may be part of SEQ ID NOS: 1, 3-19, or has at least 80% amino acid sequence identity to SEQ ID NOS: 1, 3-19.
In some embodiments, the isolated peptide may be a truncation of a cupredoxin. The isolated peptide may be more than about 10 residues and not more than about 100 residues. The isolated peptide may comprise, or alternatively consist of, Pseudomonas aeruginosa azurin residues 50-77 SEQ ID NO: 2, Pseudomonas aeruginosa azurin residues 50-67 SEQ ID NO: 25, Pseudomonas aeruginosa azurin residues 36-88 SEQ ID NO. 26, or SEQ ID NOS: 20-24.
Another aspect of the invention is a pharmaceutical composition that may comprise at least one, or two, cupredoxins or isolated peptides of the invention in a pharmaceutically acceptable carrier. The pharmaceutical composition maybe formulated for intravenous administration. In some embodiments, the cupredoxin in the pharmaceutical composition maybe from an organism such as Pseudomonas aeruginosa, Ulva pertussis, Alcaligenes faecalis, Achromobacter xylosoxidan, Bordetella bronchiseptica, Methylomonas sp., Neisseria meningitidis, Neisseria gonorrhea, Pseudomonas fluorescens, Pseudomonas chlororaphis, Xyiella fastidiosa and Vibrio par ahaernolyticus, and specifically may be from Pseudomonas aeruginosa. The cupredoxin may be SEQ ID NOS: 1 , 3-19 .
Another aspect of the invention is a method to treat a mammalian patient by administering to the patient a therapeutically effective amount of the pharmaceutical composition of the invention. The patient may be human, and may be at a higher risk to develop cancer than the general population. In some embodiments, the cancer may be melanoma, breast, pancreas, glioblastoma, astrocytoma, lung, colorectal, neck and head, bladder, prostate, skin, or eerviea! cancer. In some embodiments, the patient may have at least one high risk feature, premalignarit lesions or have been cured of cancer or premalignant lesions.
The pharmaceutical composition may be administered by intravenous injection, intramuscular injection, subcutaneous injection, inhalation, topical administration, transdermal patch, suppository, \itreous injection or oral, and specifically may be administered by intravenous injection. The pharmaceutical composition may be coadministered with at least one other chemopreventive drug, and specifically at about the same time as another chemopreventive drug.
Another aspect of the invention is a kit comprising the pharmaceutical composition of the invention in a vial. The kit may be designed for intravenous administration.
Another aspect of the invention is a method to study the development of cancer comprising contacting mammalian cells with a cupredoxin or peptide of the invention and measuring the development of premalignant and malignant cells. In some embodiments, the cells may be human and/or mammary cells. In some embodiments, the cells are induced to develop premalignant lesions.
Another aspect of the invention is an expression vector, which encodes a peptide of the invention.
Another aspect of the invention is a complex comprising a cargo compound and an amino acid sequence, where the amino acid sequence has at least about 90% sequence identity with a cupredoxin, or a fragment thereof, the amino acid sequence, or fragment thereof, is linked to the cargo compound, and the amino acid sequence facilitates entry of the cargo compound into a mammalian cancer cell. In some embodiments, the amino acid sequence of this complex has at least about 90% amino acid sequence identity to less than a full length wild-type cupredoxin or H.8 outer membrane protein, In other embodiments, the cargo compound is protein, lipoprotein, polypeptide, peptide, polysaccharide, nucleic acid, dye, micropatiiele, iiaπoparticle, toxin and drug, In particular embodiments, the cargo is a protein or polypeptide which is linked amino acid sequence to form a fusion protein. In other particular embodiments, the cargo compound is a toxin, more particularly, the Pseudomonas aeruginosa exotoxin A. In other embodiments, the cargo is a detectable substance, more specifically one detectable by fluorimetry. microscopy, X-ray CT, MRI or ultrasound.
Finally, the invention also encompasses the complex in a pharmaceutically suitable carrier. Another aspect of the present invention is directed to a method for delivering a cargo compound into a cell. In one embodiment, this method comprises contacting a cell or cells with the above complex. In other embodiments, the ceil or cells originate from a patient suffering from cancer, and are reintroduced into the patient. In other embodiments, the cells is a cancer cell, more specifically an osteosarcoma cell, lung carcinoma cell, colon carcinoma cell, lymphoma cell, leukemia cell, soft tissue sarcoma cell, breast carcinoma cell, liver carcinoma cell, bladder carcinoma cell or prostate carcinoma cell In other embodiments, the complex is administered to a patient in a therapeutically effective amount. In other embodiments, the complex is administered intravenously, topically, subcutaneous Iy, intramuscularly or into a tumor. In other embodiments, the complex is co-administered with another cancer treatment. In yet other embodiments, RNAi approaches, drug resistance, hematopoietic gene transfer, homologous recombination, ribozyme technology, antisense technology, tumor immunotherapy and tumor suppressors.translational research, cancer therapy, gene delivery systems (viral and non- viral), anti-gene therapy (antisense, siRNA & ribozymes), apoptosis; mechanisms and therapies , vaccine development, immunology and immunotherapy, and DNA synthesis and repair are used in the context of delivering DNA and/or RNA as cargo compounds in the complexes of the present invention. In a particular embodiment, the cargo compound is an antisense molecule.
Another aspect of the invention is a method to diagnose cancer. In some embodiments, the complex with a cargo that is a detectable substance is administered to a patient with cancer and the location of the cargo is detected. In particular embodiments, the cargo compound is an X-ray contrast agent and is detected by X-ray CT, the cargo compound is a magnetic resonance imaging contrast agent and is detected by MRI, and the cargo is an ultrasound contrast agent and is detectable by ultrasound, In other embodiments, the a cell or cells are contacted with a complex with a detectable substance and the location of the cargo is detected.
Another aspect of the invention is a kit that contains any of the above complexes. In some embodiments, the kit further comprises a pharmaceutically acceptable adjuvant or excipient. In other embodiments, the kit further comprises a vehicle for administration of the reagent.
These and other aspects, advantages, and features of the invention will become apparent from the following figures and detailed description of the specific embodiments. BRIEF DESCRIPTION OF THE SEQUENCES
SEQ ID NO: 1. Amino acid sequence of azurin from Pseudomonas aeruginosa (Ala GIu Cys Ser VaI Asp Be GJn GIy Asn Asp GIn Met GIn Phe Asn Thr Asn Ala He Tlir VaI Asp Lys Ser Cys Lys GIn Phe Thr VaI Asn Leu Ser His Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp Ser Arg VaI lie Ala His Thr Lys Leu He GIy Ser GIy GIu Lys Asp Ser VaI Thr Phe Asp VaI Ser Lys Leu Lys GIu GIy GIu GIn Tyr Met Phe Phe Cys Thr Phe Pro GIy His Ser Ala Leu Met Lys GIy Thr Leu Thr Leu Lys). SEQ 3D NO: 2. Amino acid sequence of p28, Pseudomonas aeruginosa azurin residues 50-77 (Leu Ser Thr Ala AIa Asp Met GIn GIy VaI VaI Thr Asp GIy Met AIa
Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp).
SEQ ED NO: 3. Amino acid sequence of plastocyanin from Phormidium laminosum (GIu Thr Phe Thr VaI Lys Met GIy Ala Asp Ser GIy Leu Leu Gin Phe GIu Pro Ala Asn VaI Thr VaI His Pro GIy Asp Thr VaI Lys Trp VaI Asn Asn Lys Leu Pro Pro His Asn He Leu Phe Asp Asp Lys GIn VaI Pro GIy Ala Ser Lys GIu Leu Ala Asp Lys Leu Ser His Ser GIn Leu Met Phe Ser Pro GIy GIu Ser Tyr GIu He Thr Phe Ser Ser Asp Phe Pro Ala GIy Thr Tyr Thr Tyr Tyr Cys Ala Pro His Arg GIy Ala GIy Met VaI GIy Lys He Thr VaI GIu GIy).
SEQ ID NO: 4, Amino acid sequence of rusticyanin from Thiobacillus ferrooxidans (GIy Thr Leu Asp Thr Thr Trp Lys GIu Ala Thr Leu Pro GIn VaI Lys Ala Met Leu GIu Lys Asp Thr GIy Lys VaI Ser GIy Asp Thr VaI Thr Tyr Ser GIy Lys Thr VaI His VaI VaI Ala Ala Ala VaI Leu Pro GIy Phe Pro Phe Pro Ser Phe GIu VaI His Asp Lys Lys Asn Pro Thr Leu GIu He Pro Ala GIy Ala Thr VaI Asp VaI Thr Phe He Asn Thr Asn Lys GIy Phe GIy His Ser Phe Asp lie Thr Lys Lys GIy Pro Pro Tyr Ala VaI Met Pro VaI He Asp Pro He VaI AIa GIy Thr GIy Phe Ser Pro VaI Pro Lys Asp GIy Lys Phe GIy Tyr Thr Asp Phe Thr Trp His Pro Thr Ala GIy Thr Tyr 1 yr Tyr VaI Cys GIn He Pro GIy His Ala Ala Thr GIy Met Phe GIy Lys He VaI VaI Lys).
SEQ ID NO: 5. Ammo acid sequence of psεudoazurin from Achromobacter cycloclastes (AIa Asp Phe GIu VaI His Met Leu Asn Lys GIy Lys Asp GIy Ala Met VaI Phe GIu Pro AIa Ser Leu Lys VaI AIa Pro GIy Asp Thr VaI Thr Phe He Pro Thr Asp Lys GIy His Asn VaI GIu Thr He Ly^ GIy Met He Pro Asp GIy Ala GIu Ala Phe Lys Ser Lys Ik Asn GM Asn Tyr Lys VaI Thr Phe Thr Ala Pro GIy VaI Tyr GIy- Va! Lys t> Thr Pro Hi> Tyr GIy Met GIy Met VaI GIy VaI VaI GIn VaI GIy Asp Ala Pro Ala Asn Leu Gb Ala VaI Lys GIy Ala Lys Asn Pro Lys Lys Ala GIn GIu Arg Leu Asp Ala Ala Leu Ala Ala Leu GIy Asn).
SEQ ID NO: 6. Amino acid sequence of azuπn from Λlcahgenes faecalis (Ala Cys Asp VaI Ser lie GIu GIy Asn Asp Ser Met GIn Phe Asn Thr Lys Ser Hc VaI VaI Asp Lys Thr Cys Lys GIu Phe Thr He Asn Leu Lys His Thr GIy Lys Leu Pro Lys Ala Ala Met GIy His Asn VaI VaI VaI Ser Lys Lys Ser Asp GIu Ser Ala VaI Ala Thr Asp GIy Met Lys Ala GIy Leu Asn Asn Asp Tyr VaI Lys Ala GIy Asp GIu Arg VaI He Ala His Thr Ser VaI lie GIy GIy GIy GIu Thr Asp Ser VaI Thr Phe Asp VaI Ser Lys Leu Lys GIu GIy GIu Asp Tyr Ala Phe Phe Cys Ser Phe Pro GIy His Trp Ser He Met Lys GIy Thr He GIu Leu GIy Ser). SEQ ID NO: 7. Amino acid sequence of azurin from Achromobacter xylosoxidans ssp. denitrificans I (Ala GIn Cys GIu Ala Thr He GIu Ser Asn Asp Ala Met GIn Tyr Asn Leu Lys GIu Met VaI VaI Asp Lys Ser Cys Lys GIn Phe Thr VaI His Leu Lys His VaI GIy Lys Met Ala Lys VaI Ala Met GIy His Asn Trp VaI Leu Thr Lys GIu Ala Asp Lys GIn GIy VaI Ala Thr Asp GIy Met Asn AIa GIy Leu AIa GIn Asp Tyr VaI Lys Ala GIy Asp Thr Arg VaI He Ala His Thr Lys VaI He GIy GIy GIy GIu Ser Asp Ser VaI Thr Phe Asp VaI Ser Lys Leu Thr Pro GIy GIu Ala Tyr Ala Tyr Phe Cys Ser Phe Pro GIy His Trp Ala Met Met Lys GIy Thr Leu Lys Leu Ser Asn).
SEQ ID NO: 8. Amino acid sequence of azurin from Bordetella bronchiseptica (Ala GIu Cys Ser VaI Asp He Ala GIy Thr Asp GIn Met GIn Phe Asp Lys Lys Ala He GIu VaI Ser Lys Ser Cys Lys GIn Phe Thr VaI Asn Leu Lys His Thr GIy Lys Leu Pro Arg Asn VaI Met GIy His Asn Trp VaI Leu Thr Lys Thr AIa Asp Met GIn Ala VaI GIu Lys Asp GIy He Ala Ala GIy Leu Asp Asn GIn Tyr Leu Lys Ala GIy Asp Thr Arg VaI Leu AIa His Thr Lys VaI Leu GIy GIy GIy GIu Ser Asp Ser VaI Thr Phe Asp VaI Ala Lys Leu Ala AIa GIy Asp Asp Tyr Thr Phe Phe Cys Ser Phe Pro GIy His GIy Ala Leu Met Lys GIy Thr Leu Lys Leu VaI Asp).
S£Q ID NO: 9. Amino acid sequence of azurin from Mcthyϊomonas sp. J (Ala Ser Cys Gk Thr Thr VaI Thr Ser GIy Asp Thr Met Thr Tyr Ser Thr Arg Ser He Ser VaI Pro AIa Ser Cys Ala GIu Phe Thr VaI Asn Phe GIu His Lys GIy His Met Pro Lys Thr GIy Met GIy His Asn Trp VaI Leu Ala Lys Ser Ala Asp VaI GIy Asp VaI Ala Lys GIu GIy Ala His Ala GIy Ala Asp Asn Asn Phe VaI Thr Pro GIy Asp Lys Arg VaI He Ala Phe Thr Pro He He GIy Gh GIy Giu Lys Thr Ser VaI Lys Phe L>s VaI Ser Ala Leu Ser Lys Asp GIu Ala Tyr Thr Tyr Phe C\s Ser lyr Pro Giy His Phe Set Met Met Arg GIy Ilir Leu Lys Leu GIu GIu). SEQ ID NO: 10. Amino acid sequence of azurin from Neisseria meningitidis Z2491 (Cys Ser GIn GIu Pro Ala Ala Pro Ala Ala GIu Ala Thr Pro Ala Ala GIu Ala Pro Ala Ser GIu Ala Pro Ala Ala GIu Ala Ala Pro Ala Asp Ala Ala GIu Ala Pro Ala Ala GIy Asn Cys Ala Ala Thr VaI GIu Ser Asn Asp Asn Met GIn Phe Asn Thr Lys Asp He GIn Vai Ser Lys Ala Cys Lys GIu Phe Thr He Thr Leu Lys His Thr GIy Thr GIn Pro Lys Thr Ser Met GIy His Asn He VaI lie GIy Lys Thr GIu Asp Met Asp GIy He Phe Lys Asp GIy VaI GIy Ala Ala Asp Thr Asp Tyr VaI Lys Pro Asp Asp Ala Arg VaI VaI Ala His Thr Lys Leu He GIy GIy GIy GIu GIu Ser Ser Leu Thr Leu Asp Pro Ala Lys Leu Ala Asp GIy GIu Tyr Lys Phe Ala Cys Thr Phe Pro GIy His GIy Ala Leu Met Asn GIy Lys VaI Thr Leu VaI Asp). SEQ ID NO: 1 1. Amino acid sequence of azurin from Pseudomonas fluorescen (Ala
GIu Cys Lys Thr Thr He Asp Ser Thr Asp GIn Met Ser Phe Asn Thr Lys Ala He GIu He Asp Lys Ala Cys Lys Thr Phe Thr VaI GIu Leu Thr His Ser GIy Ser Leu Pro Lys Asn VaI Met GIy His Asn Leu VaI He Ser Lys GIn Ala Asp Met GIn Pro He Ala Thr Asp GIy Leu Ser Ala GIy lie Asp Lys Asn Tyr Leu Lys GIu GIy Asp Thr Arg VaI He Ala His Thr Lys VaI He GIy Ala GIy GIu Lys Asp Ser Leu Thr He Asp VaI Ser Lys Leu Asn Ala Ala GIu Lys Tyr GIy Phe Phe Cys Ser Phe Pro GIy His He Ser Met Met Lys GIy Thr VaI Thr Leu Lys).
SEQ ID NO: 12. Amino acid sequence of azurin from Pseudomonas chloromphis (Ala GIu Cys Lys VaI Asp VaI Asp Ser Thr Asp GIn Met Ser Phe Asn Thr Lys GIu He Thr ϊle Asp Lys Ser Cys Lys Thr Phe Thr VaI Asn Leu Thr His Ser GIy Ser Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Lys Ser Ala Asp Met Ala GIy He Ala Thr Asp GIy Met Ala Ala GIy lie Asp Lys Asp Tyr Leu Lys Pro GIy Asp Ser Arg VaI He Ala His Thr Lys He He GIy Ser GIy GIu Lys Asp Ser VaI Thr Phe Asp VaI Ser Lys Leu Thr Ala GIy GIu Ser Tyr GIu Phe Phe Cys Ser Phe Pro GIy His Asn Ser Met Met Lys GIy Ala VaI VaI Leu Lys).
SEQ ID NO: 13. Amino acid sequence of azurin from Xylelia fastidiosa 9a5c (Lys Thr Cys Ala VaI Thr He Ser AIa Asn Asp GIn Met Lys Phe Asp GIn Asn Thr IJe Lys He Ala Ala GIu Cys Thr His VaI Asn Leu Thr Leu Thr His Thr GI> Lys Lys Ser Ala Arg VaI Met GIy His Asn Trp VaI Leu Thr Lys Thr Thr Asp Met GIn Ala VaI Ala Leu Ala GIy Leu His Ala Thr Leu AIa Asp Asn Tyr VaI Pro Lys Ala Asp Pro Arg VaI He Ala His Thr Ala lie lie GIy GIy GIy GIu Arg Thr Ser He Thr Phe Pro Thr Asn Thr Leu Ser Lys Asn VaI Ser Tyr Thr Phe Phe Cys Ser Phe Pro GIy His Trp AIa Leu Met Lys GIy Thr Leu Asn Phe GIy GIy).
SEQ ID \Q- 14, Amino acid sequence of stellacyanm from Cueumis saiivus (Met Gin Ser Thr VaI His He VaI GIy Asp 4sn Thr GSy Trp Ser Va! Pro Ser Ser Pro Asn Phe Tyr Ser GIn Tip Ala Ala GIy Lys Thr Phe Arg VaI GIy Asp Ser Leu GIn Phe Asn Phe Pro Ala Asn Ala His Asn VaI His GIu Met GIu Thr Lys GIn Ser Phe Asp Ala Cys Asn Phe VaI Asn Ser Asp Asn Asp VaI GIu Arg Thr Ser Pro Va! He GIu Arg Leu Asp GIu Leu GIy Met His Tyr Phe VaI Cys Thr VaI GIy Thr His Cys Ser Asn GIy GIn Lys Leu Ser lie Asn VaI VaI Ala Ala Asn Ala Thr VaI Ser Met Pro Pro Pro Ser Ser Ser Pro Pro Ser Ser VaI Met Pro Pro Pro VaI Met Pro Pro Pro Ser Pro Ser).
SEQ ID NO: 15. Amino acid sequence of auraeyanin A from Chloroflexus auranttacus (Met Lys He Thr Leu Arg Met Met VaI Leu Ala VaI Leu Thr Ala Met Ala Met VaI Leu Ala Ala Cys GIy GIy GIy GIy Ser Ser GIy GIy Ser Thr GIy GIy GIy Ser GIy Ser GIy Pro VaI Thr He GIu He GIy Ser Lys GIy GIu GIu Leu Ala Phe Asp Lys Thr GIu Leu Thr VaI Ser Ala GIy GIn Thr VaI Thr He Arg Phe Lys Asn Asn Ser Ala VaI GIn GIn His Asn Trp He Leu VaI Lys GIy GIy GIu Ala GIu Ala Ala Asn He Ala Asn Ala GIy Leu Ser Ala GIy Pro Ala Ala Asn Tyr Leu Pro Ala Asp Lys Ser Asn He He Ala GIu Ser Pro Leu Ala Asn GIy Asn GIu Thr VaI GIu VaI Thr Phe Thr Ala Pro Ala Ala GIy Thr Tyr Leu Tyr lie Cys Thr VaI Pro GIy His Tyr Pro Leu Met GIn GIy Lys Leu VaI VaI Asn).
SEQ ID NO: 16. Amino acid sequence of auraeyanin B from Chloroflexus aurantiacus (Ala Ala Asn Ala Pro GIy GIy Ser Asn VaI VaI Asn GIu Thr Pro Ala GIn Thr VaI GIu VaI Arg AIa Ala Pro Asp Ala Leu Ala Phe Ala GIn Thr Ser Leu Ser Leu Pro Ala Asn Thr VaI VaI Arg Leu Asp Phe VaI Asn GIn Asn Asn Leu GIy VaI GIn His Asn Trp VaI Leu VaI Asn GIy GIy Asp Asp VaI Ala Ala Ala VaI Asn Thr Ala Ala GIn Asn Asn Ala Asp Ala Leu Phe VaI Pro Pro Pro Asp Thr Pro Asn Ala Leu Ala Trp Thr AIa Met Leu Asn Ala GIy GIu Ser GIy Ser VaI Thr Phe Arg Thr Pro Ala Pro GIy Thr Tyr Leu Tyr He Cys Thr Phe Pro GIy His Tyr Leu Ala GIy Met Lys GIy Thr Leu Thr VaI Thr Pro).
SEQ ID KO: 17. Amino acid sequence of cucumber basic protein from Cucumis sativus (Ala VaI Tyr VaI VaI GIy Gl> Ser GIy GIy Trp Thr Phe Asn Thr GIu Ser Trp Pro Lys GIy Lys Arg Phe Arg Ala GIy Asp He Leu Leu Phe Asn Tyr Asn Pro Ser Met His Asn VaI VaI VaI VaI Asn GIn GIy GIy Phe Ser Thr Cys Asn Thr Pro Ala GIy Ala L>s VaI Tyr Thr Ser GIy Arg Asp GIn lie Lys Leu Pro Lys GIy GIn Ser Tyr Phe He Cys Asn Phe Pro GIy His Cys GIn Ser GIy Met Lys He Ala VaI Asn AIa Leu). SEQ ID NO: 18. Amino acid sequence of Laz from Neisseria gonorrhoeae F62 (Cys
Ser Gin GIu Pro Ma Ala Pro Aϊa AIa GIu 41a Thr Pro AIa Gl> GIu Ala Pro Ala Ser GIu Λla Pro Ala Ala GIu Ala AIa Pro Ala Asp AIa Ala GIu Ala Pro AIa Ala GIy Asn C> Ala AIa Thr VaI GIu Scr Asn Asp Asn Met GIn Phe Asn Thr Lys Asp He GIn VaI Ser Lys AIa Cys Lys Glυ Phe Thr He Thr Leu Lys His Thr GIy Thr GIn Pro Lys Ala Ser Met GIy His Asn Leu VaI lie Ala Lys Ala GIu Asp Met Asp GIy VaI Phe Lys Asp GIy VaI GIy Ak Ala Asp Thr Asp Tyr VaI Lys Pro Asp Asp Ala Arg VaI VaI Ala His Thr Lys Leu He GIy GIy GIy GIu GIu Ser Ser Leu Thr Leu Asp Pro Ala Lys Leu AJa Asp GIy Asp Tyr Lys Phe Ala Cys Thr Phe Pro GIy His GIy Ala Leu Met Asn GIy Lys VaI Thr Leu VaI Asp).
SEQ ID NO: 19. Amino acid sequence of the azurin from Vibrio parahaemolyticus (Met Ser Leu Arg He Leu Ala Ala Thr Leu Ala Leu Ala GIy Leu Ser Phe GIy Ala GIn Ala Ser Ala GIu Cys GIu VaI Ser He Asp Ala Asn Asp Met Met GIn Phe Ser Thr Lys Thr Leu Ser VaI Pro Ala Thr Cys Lys GIu VaI Thr Leu Thr Leu Asn His Thr GIy Lys Met Pro Ala GIn Ser Met GIy His Asn VaI VaI He Ala Asp Thr Ala Asn He GIn Ala VaI GIy Thr Asp GIy Met Ser Ala GIy Ala Asp Asn Ser Tyr VaI Lys Pro Asp Asp GIu Arg VaI Tyr Ala His Thr Lys VaI VaI GIy GIy GIy GIu Ser Thr Ser He Thr Phe Ser Thr GIu Lys Met Thr A3a GIy GIy Asp Tyr Ser Phe Phe Cys Ser Phe Pro GIy His Trp Ala He Met GIn GIy Lys Phe GIu Phe Lys), SEQ HD NO: 20. Amino acid sequence of amino acids 57 to 89 of auracyanin B of
Chloroflcxus aurantiacus (His Asn Trp VaI Leu VaI Asn GIy GIy Asp Asp VaI Ala Ala Ala VaI Asn Thr Ala Ala GIn Asn Asn Ala Asp Ala Leu Phe Va! Pro Pro Pro Asp).
SEQ ID NO: 21. Amino acid sequence of amino acids 51-77 of Ps eudomonas syringae azurin (Ser Lys Lys AIa Asp Ala Ser Ala He Thr Thr Asp GIy Met Ser VaI GIy He Asp Lys Asp Tyr VaI Lys Pro Asp Asp).
SEQ ID NO: 22. Amino acid sequence of amino acids 89-115 of Neisseria meningitidis Laz (He GIy Lys Thr GIu Asp Met Asp GIy He Phe Lys Asp GIy VaI GIy AIa AIa Asp Thr Asp Tyr VaI Lys Pro Asp Asp).
SEQ ID NO: 23. Amino acid sequence of amino acids 52-78 of Vibrio parahaemolyticus azurin (AIa Asp Thr Ala Asn He GIn Ala VaI GIy Thr Asp GIy Met Ser Ala GIy Ala Asp Asn Ser Tyr VaI Lys Pro Asp Asp).
SEQ ID NO: 24. Amino acid sequence of amino acids 51 -77 of BordeicHa brβnchiseptica azurin (Thr Lys Thr AIa Asp Met GIn Ala VaI GIu Lys Asp GIy He Ala Ala GIy Leu Asp Asn GIn Tyr Leu Lys Ala GIy Asp). SEQ ID NO: 25. Amino acid sequence of pi 8, Pscudomonas aeruginosa azurin residues 50-67 (Leu Ser Thr Ala Ala Asp Met Gk GIy VaI VaI Thr Asp Gh Met Ala Ser Gl> } SEQ ID NO: 26. Amino acid sequence of amino acids 36-88 of Pseudomonas aeruginosa azurin (Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp Ser Arg VaI He Ala His Thr Lys Leu He GIy). SEQ ID NO: 27. Amino acid sequence of amino acids 36 to 77 of Pseudomonas aeruginosa azurin (Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp).
SEQ ID NO: 28. Amino acid sequence of amino acids 36 to 89 of Pseudomonas aeruginosa azurin (Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp Ser Arg VaI lie Ala His Thr Lys Leu He GIy Ser).
SEQ ID NO: 29. Amino acid sequence of amino acids 36 to 128 of Pseudomonas aeruginosa azurin (Pro GIy Asn Leu Pro Lys Asn VaI Met GIy His Asn Trp VaI Leu Ser Thr Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys Asp Tyr Leu Lys Pro Asp Asp Ser Arg VaI He Ala His Thr Lys Leu He GIy Ser GIy GIu Lys Asp Ser VaI Thr Phe Asp VaI Ser Lys Leu Lys GIu GIy GIu GIn Tyr Met Phe Phe Cys Thr Phe Pro GIy His Ser Ala Leu Met Lys GIy Thr Leu Thr Leu Lys).
SEQ ID NO: 30. Amino acid sequence of amino acids 53 to 70 of Pseudomonas aeruginosa azurin (Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met Ala Ser GIy Leu Asp Lys).
SEQ HD NO: 31. Amino acid sequence of amino acids 53 to 64 of Pseudomonas aeruginosa azurin (Ala Ala Asp Met GIn GIy VaI VaI Thr Asp GIy Met).
SEQ ID NO: 32. Amino acid sequence DGXXXXXDXXYXKXXD. SEQ ID NO: 33. Amino acid sequence DGXXXXDXXYXKXXD. BRIEF DESCRIPTION OF THE FIGURES
Figure 1. Figure 1 depicts photographs of all of the glands evaluated for the efficacy of p28 and azuπn. Figure IA shows a representative photograph of alveolar lesions in a DMBA-treated gland and its comparison with a gland that was treated with DMBA along with a chemopreventive agent. Figures IB- IF show representative photographs of the effects of p28 on the development of aheolar lesions.
Figure 2. Figure 2 depicts a graph showing the efficacy of p28 against DMBA- induced mammary alveolar lesions. Figure 3. Figure 3 depicts photographs of representative sections of ductal lesions and effect of p28.
Figure 4. Figure 4 depicts a graph showing the efficacy of p28 against DMBA- induced ductal lesions
Figure 5. Diagram showing the localization of the α-helix in wt-azurin as well as in the wt-azurin 50-77 protein transduction domain. Replacement of three amino acids in the azurin 50-77 domain by proline residues is indicated.
Figure 6 (A), (B) and (C). (A) Diagram showing construction of a GST-GFP-azu 50-77 fusion protein. The gfp gene was introduced at the 3'-end of the gst gene (for GST- GFP) and the azu 50-77 fragment was then Iigated at the 3!-end of the gfp gene in frame to produce the GST-GFP-azu 50-77 fusion protein. GST-GFP-azu 50-77 was purified as a single fusion protein from the cell lysates. Purified proteins were run on SDS-PAGE and detected by Coomassie Blue staining (6(B) and also by Western blotting using anti-azurin antibody (6(C)).
Figure 7 (A), (B) and (C). Diagrams showing a kinetic study for the internalization of GST-Green Fluorescent Protein (GFP) and GST-GFP-azunn fusion proteins. Green fluorescence was assayed in J774 ceils treated with various concentrations of GST-GFP (10(a)) or GST-GFP-azu 50-77 (IG(B)) at 37°C for 1 hr. Ten thousand cells were analyzed by flow cytometry, (c) Time-dependence of internalization of GST-GFP-azu 50-77. J774 cells were incubated with 200 μg/tnl GST-GFP-azu 50-77 for indicated times at 37°C and analyzed by flow cytometry.
Figure 8 (A), (B) and (C). (A) Diagram showing the exotoxin A domain ΪIΪ (ammo acids 405-M3). as well as part of domain Ib (amino acids 381-404), fused to GSl (GST- PEDIII) as earlier described for the GST-GFP fusion. The azu 50-77 fragment was then ligated to the carboxyl end of GST-PEDIII (GST-PEDIII-azu 50-77), using PCR. (B) The fusion proteins were purified by glutathione Sepharose 4B column gel filtration column chromatography and ran on SDS-PAGE for size determination. (C) Diagram showing action of GST-PEDΪII-azu 50-77 fusion protein in UISO-Mel-2 cancer cells and in normal fibroblast (FBT) cells, as determined by PEDlII-mediated cytotoxicity. Various concentrations, as indicated, of GST-PEDIII and GST-PEDIII-azu 50-77 were incubated with UISO-Mel-2 and FBT cells for 24 h, after which the cell viability was determined by MTT assay.
Figure 9. Diagram PEDHI-rnediated cytotoxicity of GST-PED Ill-rusticyanin fusion protein against UISO-Mel-2 cancer cells and FBT cells. Various concentrations, as indicated. of GST-PEDIII and GST-PEDIII-azu 50-77 were incubated with UISO-Mel-2 and FBT cells for 24 h, after which the cell viability was determined by MTT assay.
DETAILED DESCRIPTION OF THE INVENTION Definitions
As used herein, the term "cell" includes either the singular or the plural of the term, unless specifically described as a "single cell."
As used herein, the terms "polypeptide," "peptide," and "protein" are used interchangeably to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid. The terms also apply to naturally occurring amino acid polymers. The terms "polypeptide," "peptide," and "protein" are also inclusive of modifications including, but not limited to. glycosylation, lipid attachment, sulfation, gamma- carboxylation of glutamic acid residues, hydroxylation and ADP-ribosylation. It will be appreciated thai polypeptides are not always entirely linear. For instance, polypeptides may be branched as a result of ubiquitination and they may be circular (with or without branching), generally as a result of post-translation events, including natural processing event and events brought about by human manipulation which do not occur naturally. Circular, branched and branched circular polypeptides may be synthesized by non-translation natural process and by entirely synthetic methods as well.
As used herein, the term "pharmacologic activity" means the effect of a drug or other chemical on a biological system, The effect of chemical may be beneficial {therapeutic) or harmful (toxic). The pure chemicals or mixtures maybe of natural origin (plant, animal, or mineral) or may be synthetic compounds.
As used herein, the term "premalignant" means precancerous, or before abnormal cells divide without control. As used herein, the term "lesion" means an area of abnormal tissue.
As used herein, the term "pathological condition" includes anatomic and physiological deviations from the normal that constitute an impairment of the normal state of the living animal or one of its parts, that interrupts or modifies the performance of the bodily functions, and is a response to various factors (as malnutrition, industrial hazards, or climate), to specific infective agents (as worms, parasitic protozoa, bacteria, or viruses), to inherent defects of the organism (as genetic anomalies), or to combinations of these factors.
As used herein, the term "condition" includes anatomic and physiological deviations from the normal that constitute an impairment of the normal state of the living animal or one of its parts, that interrupts or modifies the performance of the bodily functions. As used herein, the term "suffering from" includes presently exhibiting the symptoms of a pathological condition, having a pathological condition even without observable symptoms, in recovery from a pathological condition, or recovered from a pathological condition.
As used herein, the term "chemoprevention" is the use of drugs, vitamins, or other agents to try to reduce the risk of, or delay the development or recurrence of, cancer.
A used herein, the term "treatment" includes preventing, lowering, stopping, or reversing the progression or severity of the condition or symptoms associated with a condition being treated. As such, the term "treatment" includes medical, therapeutic, and/or prophylactic administration, as appropriate. Treatment may also include preventing or lessening the development of a condition, such as cancer.
As used herein, the term "inhibit cell growth"' means the slowing or ceasing of cell division and or cell expansion. This term also includes the inhibition of cell development or increases in cell death.
A "therapeutically effective amount" is an amount effective to prevent, lower, stop or reverse the development of, or to partially or totally alleviate the existing symptoms of a particular condition for which the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled m the art The term "substantially pure," as used herein, when used to modify a protein or other cellular product of the invention, refers to, for example, a protein isolated from the growth medium or cellular contents, in a form substantially free of, or unadulterated by. other proteins and/or other compounds. The term ""substantially pure" refers to a factor in an amount of at least about 75%, by dry weight, of isolated fraction, or at least "75% substantially pure."' More specifically, the term "substantially pure" refers to a compound of at least about 85%, by dry weight, of isolated fraction, or at least ''85% substantially pure.'' Most specifically, the term "substantially pure" refers to a compound of at least about 95%, by dry weight, of isolated fraction, or at least "95% substantially pure." The term "substantially pure" may also be used to modify a synthetically-made protein or compound of the invention, where, for example, the synthetic protein is isolated from the reagents and byproducts of the synthesis reaction(s).
The term "pharmaceutical grade," as used herein, when referring to a peptide or compound of the invention, is a peptide or compound that is isolated substantially or essentially from components which normally accompany the material as it is found in its natural state, including synthesis reagents and by-products, and substantially or essentially isolated from components that would impair its use as a pharmaceutical. For example, a "pharmaceutical grade" peptide may be isolated from any carcinogen. In some instances, "pharmaceutical grade" may be modified by the intended method of administration, such as "intravenous pharmaceutical grade," in order to specify a peptide or compound that is substantially or essentially isolated from any substance that would render the composition unsuitable for intravenous administration to a patient. For example, an "intravenous pharmaceutical grade" peptide may be isolated from detergents, such as SDS, and antibacterial agents, such as azide, The terms "isolated," "purified" or "biologically pure" refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment. An "isolated" region of a polypeptide refers to a region that does not include the whole sequence of the polypeptide from which the region was derived. An "isolated" nucleic acid, protein, or respective fragment thereof has been substantially removed from its in vho environment so that it maj be manipulated by the skilled artisan, such as but not limited to, nucleotide sequencing, restriction digestion, site-directed mutagenesis, and subcloning into expression vectors for a nucleic acid fragment as well as obtaining the protein or protein fragment in substantially pure quantities.
The term "variant" as used herein with respect to a peptide, refers to amino acid sequence variants which may have amino acids replaced, deleted, or inserted as compared to the wild-type polypeptide. Variants may be truncations of the wild-type peptide. A "deletion'' is the removal of one or more amino acids from within the polypeptide, which a "truncation" is the removal of one or more amino acids from one or both ends of the polypeptide. Thus, a variant peptide may be made by manipulation of genes encoding the polypeptide. A variant may be made by altering the basic composition or characteristics of the polypeptide, but not at least some of its pharmacologic activities. For example, a "variant" of azurin can be a mutated azurin that retains its ability to inhibit the development of premalignant mammalian cells. In some cases, a variant peptide is synthesized with non- natural amino acids, such as ε-(3,5-dinitrobenzoyl)-Lys residues. Ghadiri & Fernholz, J. Am. Chem. Soc., 112:9633-9635 (1990). In some embodiments, the variant has not more than 20 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. In some embodiments, the variant has not more than 15 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. In some embodiments, the variant has not more than 10 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. In some embodiments, the variant has not more than 6 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. In some embodiments, the variant has not more than 5 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. In some embodiments, the variant has not more than 3 amino acids replaced, deleted or inserted compared to wild-type peptide or part thereof. The term ''amino acid," as used herein, means an amino acid moiety that comprises any naturally-occurring or non-natural Iy occurring or synthetic amino acid residue, i.e.. any moiety comprising at least one carboxyl and at least one amino residue directly linked b> one. two three or more carbon atoms, typically one (α) carbon atom.
The term "derivative" as used herein with respect to a peptide refers to a peptide that is derived from the subject peptide. A derivation includes chemical modifications of the peptide such that the peptide still retains some of its fundamental activities. For example, a "derivative" of azuπn can, for example, be a chemically modified azurin that retains its ability to inhibit angiogenesis in mammalian cells. Chemical modifications of interest include, but are not limited to. amidation, acetylation, sulfation, polyethylene glycol (PEG) modification, phosphorylation or glycosylation of the peptide. In addition, a derivative peptide may be a fusion of a polypeptide or fragment thereof to a chemical compound, such as but not limited to, another peptide, drug molecule or other therapeutic or pharmaceutical agent or a detectable probe.
The term "percent (%) amino acid sequence identity" is defined as the percentage of amino acid residues in a polypeptide that are identical with amino acid residues in a candidate sequence when the two sequences are aligned. To determine % amino acid identity, sequences are aligned and if necessary, gaps are introduced to achieve the maximum % sequence identity; conservative substitutions are not considered as part of the sequence identity. Amino acid sequence alignment procedures to determine percent identity are well known to those of skill in the art. Often publicly available computer software such as BLAST, BLAST2, ALIGN2 or Megalign (DNASTAR) software is used to align peptide sequences. In a specific embodiment, Blastp (available from the National Center for Biotechnology Information, Bethesda MD) is used using the default parameters of long complexity filter, expect 10, word size 3, existence 11 and extension 1.
When amino acid sequences are aligned, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) can be calculated as:
% amino acid sequence identity = XY* 100 where X is the number of amino acid residues scored as identical matches by the sequence alignment program's or algorithm's alignment of A and B and
Y is the total number of amino acid residues in B,
If the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A. When comparing longer sequences to shorter sequences, the shorter sequence will be the "B" sequence. For example, when comparing truncated peptides to the corresponding wild-type polypeptide, the truncated peptide will be the "B" sequence, General
The present invention provides compositions comprising cupredoxm, and variants, derivatives and structural equivalents of cupredoxins, and methods to prevent the development of cancer in mammals. The invention also provides to variants, derivatives and structural equivalents of cupredoxin that retain the ability to prevent the development of cancer or the re-occurrence of cancer in mammals. Most particularly, the invention provides compositions comprising Pseudomonas aeruginosa azuπn, variants, derivatives and structural equivalents of azurin, and their use to treat patients, and particularly patients at a higher risk of developing cancer than the general population. Finally, the invention provides methods to study the development of cancer in mammalian cells, tissues and animals by contacting the cells with a cupredoxin, or variant, derivative or structural equivalent thereof, before or after inducing premalignant lesions, and observing the development of premalignant and/or malignant cells. Previously, it was known that a redox protein elaborated by Pseudomonas aerugisnosa^ the cupredoxin azurin, selectively enters J774 lung cancer cells but not normal cells, and induces apoptosis. Zaborina et al, Microbiology 146:2521-2530 (2000). Azurin can also selectively enter and kill human melanoma UISO-Mel-2 or human breast cancer MCF-7 cells. Yamada et al, PNAS 99:14098-14103 (2002); Punj et al., Oncogene 23:2367- 2378 (2004). Azurin from P, aeruginosa preferentially enters J774 murine reticulum cell sarcoma cells, forms a complex with and stabilizes the tumor suppressor protein p53, enhances the intracellular concentration of p53, and induces apoptosis. Yamada et al.. Infection and Immunity 70:7054-7062 (2002). Detailed studies of various domains of the azurin molecule showed that amino acids 50-77 (p28) (SEQ ID NO: 2) represented a protein transduction domain (PTD) critical for internalization and subsequent apoptotic activity. Yamada et al , Cell Microbial. 7: 1418-1431 (2005).
It is now known that azurin, and peptides derived from azurin, such as p28 and pi 8. have chemopreventive properties. It is now known that azurin, p28. prevent formation of premalignant preneoplastic lesions in mouse mammary" gland organ culture. In a mouse mammary gland organ culture model, azurin at 50 μg/ml was found to inhibit the formation of alveolar lesions by 6"70 o. Likewise, p2S at 25 μg/ml was found to inhibit the formation of alveolar lesions by 67° ό. See Example L Further, azuπri at 50 μg ml was found to inhibit the formation of ductal lesions by 79%, and p28 at 25 μg/ml inhibited the formation of ductal lesions by 71%. See Example 1, Confocal microscopy and FAC showed that azurin and p28 entered normal murine mammary epithelial cells (MM3MG) and mammary cancer cells (4Tl), P28 also entered human umbilical vein endothelial cells (HUVEC) in a temperature. time and concentration dependent manner and inhibited capillary tube formation of HUVEC plated on Matrigei*' in a dose dependent manner. Confocal microscopy and FAC also showed that pi 8 selectively entered human melanoma (Mel-2,7,29), breast (MCF- 7), ovarian (SK-O V3), pancreatic (CAPAN-2). glioblastoma (LN-229), astrocytoma (CCF-STTGl), prostate (LN-CAP), and kidney (ACHN-CRLl 61 1) cell lines. In addition, Imaging of pi 8 labeled with an infrared dye (λem 800nm) in athymic mice bearing xenografted melanoma tumors clearly demonstrated selective uptake in primary s.c. tumors and distant organ metastases without accumulating in normal organs and tissues. It is therefore now known that azurin and variants of azurin may be used to inhibit the formation of premalignant preneoplastic lesions, and thus the development of cancer, and specifically breast cancer, in mammalian patients.
Standard cancer treatment methods, including radiotherapy and chemotherapy, involve damaging the DNA of the cancer cell. The cellular response to normal DNA damage includes activation of DNA repair, cell cycle arrest and lethality (Hall, Radiobiology jor the Radiologist, Harper and Row, 1988). For example, the induction of DNA double-strand breaks results in lethal chromosomal aberrations that include deletions, dicentrics, rings, and anaphase bridges (Hall, Radiobiology for the Radiologist, Harper and Row, 1994).
Because of the selective uptake of the peptides of the present invention by tumors and various cancer cells, it is now known that these peptides, including in one embodiment, pi 8 may have use as a non- viral vector for introducing materials into tumors and cancer cells. For example, the peptides of the present invention may be used to introduce DNA or RKA fragments into a cancer cell thereby providing a therapeutic DNA or RNA fragment treatment to a tumor or cancer cell.
The following describe non-limiting exemplary techniques and/or particular DNA or RNA fragments that can be introduced with the peptides of the present invention, and, in one embodiment, pi 8. which facilitate the entry of a linked molecule into a mammalian cancer cell. For example, the present intention can be used with gene therapy, RNAi approaches. hematopoietic gene transfer, homologous recombination, ribozyme technology, antisense technology, tumor immunotherapy and tumor suppressors, translational research, anti-gene therapy (antisense, siRNA & ribozymes), apoptosis, immunology and immunotherapy, DNA synthesis and repair. Gene therapy involves the transfer of a foreign gene into a cancer cell, for example a tumor suppressor or inducer of apoptosis, under conditions suitable for expression of the gene. Once expressed, the gene product confers a beneficial effect on the tumor cell by either slowing its growth, inhibiting its metastatic potential, or killing it outright. Historically, the clinical effectiveness of cancer gene therapy has been limited by 1) lack of control of therapeutic gene expression within the tumor, and 2) selective targeting of the vector to the tumor. The compounds of the present invention address the selective targeting of tumor cells. Moreover, several strategies have been proposed for the control of gene expression. One strategy is transcriptional targeting in which the promoter regulating the therapeutic gene is activated by tumor- selective transcription factors. Examples include the use of the MUC-I promoter in breast cancer and the CEA promoter in colon cancer (Kurihara et ai, "Selectivity of a replication- component adenovirus for human breast carcinoma cells expressing the MUCl antigen," J. Clin. Invest. 106(6): 763-771, 2000; Konishi et aL, "Transcriptionally targeted in vivo gene therapy for carcinoembrionic antigen-producing adenocarcinoma," J. Med. ScL, 48(3): 79-89, 1999). Antisense techniques rely on the introduction of a nucleic acid molecule into a cell which typically is complementary to a mRNA expressed by the selected gene. The antisense molecule typically suppresses translation of the mRNA molecule and prevents the expression of the polypeptide encoded by the gene. Modifications of the antisense technique may prevent the transcription of the selected gene by the antisense molecule binding to the gene's DNA to form a triple helix. One particular antisense drug that can be used in accordance with the present invention is G3139 (also known as oblimersen; manufactured by Genta. Inc., Lexington, MA). Another particular antisense molecule that can be used is G4460 (also known as c-myb antisense manufactured by Genta, Berkeley Heights, NJ).
RNA interference (RNAi) based molecules can also be attached to the peptides of the present invention. RNAi is generally mediated b> double stranded RNA ("dsRNA"), short hairpin RNA ("shRNA") or other nucleic acid molecules with similar characteristics. These nucleic acid molecules are processed or cut into smaller pieces by cellular enzymes including Dicer and Drosha. The smaller fragments of the nucleic acid molecules can then be taken up by a protein complex (the RISC complex) that mediates degradation of mRNAs. The RISC complex will degrade mRNA that complementariiy base pairs with the nucleic acid molecules it has taken up. In this manner, the mRNA is specifically destroyed, thus preventing encoded-for proteins from being made.
Ribozyme technologies rely on the introduction of a nucleic acid molecule into a cell which expresses a RKA molecule which binds to, and catalyses the selective cleavage of, a target RNA molecule. The target RKA molecule is typically a mRNA molecule, but it may be, for example, a retroviral RNA molecule. Targeted gene deletion by homologous recombination, which requires two gene- inactivating events (one for each allele) is also a strategy that can be used with the present invention.
Particular therapies delivered in conjunction with the compounds of the present invention can also be directed against cancer-specific transcription complexes (CSTCs) that can control expression of proteins that are critical for cancer development. See, for example. United States Patent Application No. 2008/0027002 which is incorporated by reference herein for its teachings regarding cancer therapies directed against CSTCs.
Due to the high degree of structural similarity between cupredoxins, it is likely that other cupredoxins will inhibit the formation of premalignant lesions in mammals as well as azurin. Such cupredoxins may be found in, for example, bacteria or plants. Several cupredoxins are known to have pharmacokinetic activities similar to those of azurin from Pseudomonas aeruginosa. For example, rusticyanin from Thiobacillus ferrooxidans can also enter macrophages and induce apoptosis. Yaraada et al., Cell Cycle 3: i 182-1 18? (2004); Yamada et al, Cell. Micro. 7:1418-1431 (2005). Plastocyanin from Phormidium laminosum and pseudoazurin form Λchromobacter cycloclastes also are cytotoxic towards macrophages. U.S. Pat. Pub. No. 20060040269, published Feb. 23, 2006, It is therefore contemplated that other cupredoxins may be used in the compositions and methods of the invention. Further, variants, derivatives, and structural equivalents of cupredoxins that retain the ability to inhibit the formation of cancer in mammals may also be used in the compositions and methods of the invention. These variants and derivatives may include, but are not limited to, truncations of a eupredoxin. conservative substitutions of amino acids and proteins modifications such as PEGylation and all-hydrocarbon stabling of α-helices Compositions of the Invention
The invention provides for peptides that are variants, derivatives or structural equivalents of eupredoxin that inhibit the development of premalignant lesions in mammalian cells, tissues and animals. The invention further provides for peptides that are variants, derivatives or structural equivalents of eupredoxin that inhibit the development of cancer in mammalian cells, tissues and animals. In some embodiments, the peptide is isolated. In some embodiments, the peptide is substantially pure or pharmaceutical grade, In other embodiments, the peptide is in a composition that comprises, or consists essentially of, the peptide. In another specific embodiment, the peptide is non-antigenic and does not raise an immune response in a mammal, and more specifically a human. In some embodiments, the peptide is less that a full-length eupredoxin, and retains some of the pharmacologic activities of the cupredoxins. Specifically, in some embodiments, the peptide may retain the ability to inhibit the development of premalignant lesions in the mouse mammary gland organ culture. The invention also provides compositions comprising at least one peptide that is a eupredoxin, or variant, derivative or structural equivalent of a eupredoxin, specifically in a pharmaceutical composition. In specific embodiments, the pharmaceutical composition is designed for a particular mode of administration, for example, but not limited to, oral, intraperitoneal, or intravenous. Such compositions may be hydrated in water, or may be dried (such as by lyophilization) for later hydration. Such compositions may be in solvents other than water, such as but not limited to, alcohol.
The invention also provides compositions comprising peptides that are variants, derivatives or structural equivalents of eupredoxin that selectively enter cancer cells and/or tumors in mammalian cells, tissues and animals. In some embodiments, the peptide is pi 8 having SEQ ID NO. 25. In some embodiments, the peptide is a variant, derivative or structural equivalent of pi 8. In some embodiments, the composition is pi 8 coupled to DNA or RNA. In some embodiments, the DNA or RNA is a gene or a portion of a gene. In some embodiments, the DNA or RNA has a therapeutic effect once delivered.
Because of the high structural homology between the cupredoxins, it is contemplated that cupredoxins will have the same chemopre\ eπtive properties as azurin and p28. In some embodiments, the cxipredoxin is. but is not limited to. azurin, pseudoa/urin, plastocyanin. rusticyanin. auracyaπin. steliacyamn, cucumber basic protein or La/. In particularly specific embodiments, the azurin is derived from Pseudomonas aeruginosa, Alcaligenes jaecalis, Λchromobacter xylosoxidans ssp.denitrificans L Bordetella bronchiseptica^ Methylomonas sp., Neisseria meningitidis, Neisseria gonorrhea, Pseudomonas fluorescens, Pseudomonas chlororaphis , Xylella fastidiosa, Uϊva pertussis or Vibrio parahaemolγticm, In a very specific embodiment, the azurin is from Pseudomonas aeruginosa, In other specific embodiments, the cupredoxin comprises an amino acid sequence that is SEQ ID KO: 1 , 3-19.
The invention provides peptides that are amino acid sequence variants which have amino acids replaced, deleted, or inserted as compared to the wild-type cupredoxin. Variants of the invention may be truncations of the wild-type cupredoxin. In some embodiments, the peptide of the invention comprises a region of a cupredoxin that is less that the full length wild-type polypeptide. In some embodiments, the peptide of the invention comprises more than about 10 residues, more than about 15 residues or more than about 20 residues of a truncated cupredoxin. In some embodiments, the peptide comprises not more than about 100 residues, not more than about 50 residues, not more than about 40 residues, not more than about 30 residues or not more than about 20 residues of a truncated cupredoxin. In some embodiments, a cupredoxin has to the peptide, and more specifically SEQ ID NOS: 1, 3-19 as to the peptide of the invention, at least about 70% amino acid sequence identity, at least about 80% amino acid sequence identity, at least about 90% amino acid sequence identity, at least about 95% amino acid sequence identity or at least about 99% amino acid sequence identity. In specific embodiments, the variant of cupredoxin comprises P. aeruginosa azurin residues 50-77 (p28, SEQ ID NO: 2), azurin residues 50-67 (pi 8, SEQ ID NO: 25), or azurin residues 36-88 (SEQ ID NO: 26). In other embodiments, the variant of cupredoxin consists of P. aeruginosa azurin residues 50-77 (SEQ ID NO: 2), azurin residues 50-67 (SEQ ID NO: 25), or azurin residues 36-88 (SEQ ID NO: 26). In other specific embodiments, the variant consists of the equivalent residues of a cupredoxin other that azurin. It is also contemplated that other cupredoxin variants can be designed that a simitar pharmcologic activity to azurin residues 50-77 (SEQ ID NO: 2), or azurin residues 36-88 (SEQ ID NO: 26). To do this, the subject cupredoxin amino acid sequence will be aligned to the Pseudomonas aeruginosa azurin sequence using BLAST, BLAST2, ALIGN2 or Megaϋgn (DNASTAR), the relevant residues located on the P. aeruginosa azurin amino acid sequence, and the equivalent residues found on the subject cupredoxin sequence, and the equivalent peptide thus designed. In one embodiment of the invention, the cupredoxin variant contains at least amino acids 57 to 89 of auracyanin B of Chloroflexus auraniiacus (SEQ ID NO: 20). In another embodiment, the cupredoxin variant contains at least amino acids 50-67 of Pseudomonas aeruginosa azurin (SEQ ID NO 25). In another embodiment of the invention, the cupredoxin variant contains at least amino acids 51 -T of Pseudomonas syringae azurin (SEQ ID NO: 21). In another embodiment of the invention, the cupredoxin variant contains at least amino acids 89-1 15 of Neisseria meningitidis Laz (SEQ ID NO: 22). In another embodiment of the invention, the cupredoxin variant contains at least ammo acids 52-78 of Vibrio parahaemolyticits azurin (SEQ ID NO: 23). In another embodiment of the invention, the cupredoxin variant contains at least amino acids 51-77 oiBordetella bronchiseptica azurin (SEQ ID NO: 24).
The variants may also include peptides made with synthetic amino acids not naturally occurring. For example, non-naturally occurring amino acids may be integrated into the variant peptide to extend or optimize the half-life of the composition in the bloodstream. Such variants include, but are not limited to. D,L-peptides (diastereomer), (for example
Futaki et aL, J. Biol. Chem. 27ό(8):5836-40 (2001); Papo et aL, Cancer Res. 64(16):5779-86 (2004); Miller et al, Biochem. Pharmacol. 36(1): 169-76, (1987).; peptides containing unusual amino acids (for example Lee et al., J. Pept. Res. 63(2):69-84 (2004)), olefin-containing non- natural amino acid followed by hydrocarbon stapling (for example Schafmeister et al., J. Am. Chem. Soc. 122:5891-5892 (2000); Walenski et al., Science 305:1466-1470 (2004)), and peptides comprising ε-(3,5-dinitrobenzoyl)-Lys residues.
In other embodiments, the peptide of the invention is a derivative of a cupredoxin. The derivatives of cupredoxin are chemical modifications of the peptide such that the peptide still retains some of its fundamental activities. For example, a "derivative" of azurin can be a chemically modified azurin that retains its ability to inhibit the development of premaϋgnant lesions in mammalian cells, tissues or animals. Chemical modifications of interest include, but are not limited to, hydrocarbon stabling, amidation, aeetyϊatioFL sulfation, polyethylene glycol (PEG) modification, phosphorylation and glycosylation of the peptide. In addition, a derivative peptide maybe a fusion of a cupredoxin, or variant, derivative or structural equivalent thereof to a chemical compound, such as but not limited to. another peptide, drug molecule or other therapeutic or pharmaceutical agent or a detectable probe, Derivatives of interest include chemical modifications bv which the half-life in the bloodstream of the peptides and compositions of the invention can be extended or optimized, such as by several methods well known to those in the art, including but not limited to, circularized peptides (for example Monk et aL BioDrugs 19(4):261-78, (2005); DeFreest et ah, J. Pept. Res. 63(5):409-19 (2004)), N- and C- terminal modifications {for example Labrie et aL, Clin. Invest. Med. 13(5):275-8, (1990)), and olefin-containing non-natural amino acid followed by hydrocarbon stapling {for example Schafineister et a!., J. Am. Chem. Soc. 122:5891-5892 (2000); Walenski et aL Science 305:1466-1470 (2004)).
In another embodiment, the peptide is a structural equivalent of a cupredoxin. Examples of studies that determine significant structural homology between cupredoxins and other proteins include Toth et al. (Developmental Cell 1 :82-92 (2001 )). Specifically, significant structural homology between a cupredoxin and the structural equivalent may be determined by using the VAST algorithm. Gibrat et al, Curr Opin Struct Biol 6:377-385 (1996); Madej et al, Proteins 23:356-3690 (1995). In specific embodiments, the VAST p value from a structural comparison of a cupredoxin to the structural equivalent may be less than about 10~3, less than about 10"\ or less than about 10"7. In other embodiments, significant structural homology between a cupredoxin and the structural equivalent may be determined by using the DALI algorithm. Holm & Sander, J. MoI. Biol. 233:123-138 (1993). In specific embodiments, the DALI Z score for a pairwise structural comparison is at least about 3.5, at least about 7.0, or at least about 10.0. It is contemplated that the peptides of the composition of invention may be more than one of a variant, derivative and/or structural equivalent of a cupredoxin. For example, the peptides may be a truncation of azurin that has been PEGylated, thus making it both a variant and a derivative. In one embodiment, the peptides of the invention are synthesized with α.α- disubstituted non-natural amino acids containing olefϊn-bearing tethers, followed by an all- hydrocarbon "'staple" by ruthenium catalyzed olefin metathesis. Scharmεister et al.Λ J. Am, Chem. Soc. 122:5891 -5892 (2000); Walensky et aL, Science 305:1466-1470 (2004). Additionally, peptides that are structural equivalents of azurin may be fused to other peptides, thus making a peptide that is both a structural equivalent and a derivative. These examples are merely to illustrate and not to limit the invention. Variants, derivatives or structural equivalents of cupredoxin may or may not bind copper.
In some embodiments, the cupredoxin. or variant, derivative or structural equivalent thereof has some of the pharmacologic activities of the P aeruginosa azurin, and specifically
-?S- p28. In a specific embodiment, the cupredoxins and variants, derivatives and structural equivalents of cupredoxins that may inhibit prevent the development of premalignant lesions in mammalian cells, tissues or animals, and specifically but not limited to. mammary gland cells. The invention also provides for the cupredoxins and variants, derivatives and structural equivalents of cupredoxins that may have the ability to inhibit the development of mammalian premahgnant lesions, and specifically but not limited to. melanoma, breast, pancreas, glioblastoma, astrocytoma, lung, colorectal, neck and head, bladder, prostate, skin and cervical cancer cells. Inhibition of the development of cancer cells is any decrease, or lessening of the rate of increase, of the development of premalignant lesions that is statistically significant as compared to control treatments.
Because it is now known that cupredoxins can inhibit the development of premalignant lesions and ultimately cancer in mammalian cells, tissues or animals, and specifically breast cells, and more specifically, mouse mammary gland cells, it is now possible to design variants and derivatives of cupredoxins that retain this chemopreventive activity. Such variants, derivatives and structural equivalents can be made by, for example, creating a "library" of various variants, derivatives and structural equivalents of cupredoxins and cupredoxin derived peptides and then testing each for chemopreventive activity, and specifically chemopreventive activity in the mouse mammary gland organ culture using one of many methods known in the art, such the exemplary method in Example 1. It is contemplated that the resulting variants, derivatives and structural equivalents of cupredoxins with chemopreventive activity may be used in the methods of the invention, in place of or in addition to azurin or p28.
In some specific embodiments, the variant, derivative or structural equivalent of cupredoxin may inhibit the development of 7,12-dimethylbenz (a) anthracene (DMBA) induced premaligπant lesions in a mouse mammary gland organ culture (MMOC) to a degree that is statistically different from a non-treated control, A peptide can be tested for this activity by using the MMOC model system is descπbed m Example 1 , or as in Mehta et al (J Natl Cancer Inst 93: 1 103-1106 (2001 )) and Mehta e/ α/, (Meth Cell Sci 19:19-24 (199?)).. Other methods to determine whether cancer development is inhibited another are well known in the art and may be used as well,
In some specific embodiments, the derivative or structural eqimalent of cupredoxin inhibits the dev elopment of mammary alveolar lesions (MAI ) in the a M1VlOC model to a degree that is statistically different from a non-treated control. In some specific embodiments, the variant, deπvative or structural equivalent of cupredoxin inhibits the development of mammary ductal lesions (MDL) in the a MMOC model to a degree that is statistically different from a non-treated control. A peptide can be tested for these activities by using the MMOC model system induced to form premalignant lesions by DMBA, as described in Example 1. Evaluation of development of premalignant lesions in a MMOC model system may be determined by morphometic analysis, or histopathological analysis, as provided in Example 1 ,
In some specific embodiments, the variant, derivative or structural equivalent can selectively enter cancer cells and/or tumors in mammalian cells, tissues and animals. In some embodiments, the variant is a derivative or structural equivalent of pi 8. In some embodiments, the variant, derivative or structural equivalent can selectively enter cancer cells andor tumors in mammalian cells, tissues and animals and deliver DNA or RNA. In some embodiments, the DNA or RNA is a gene or a portion of a gene. In some embodiments, the DNA or RNA has a therapeutic effect once delivered.
Cupredoxins
These small blue copper proteins (cupredoxins) are electron transfer proteins (10-20 kDa) that participate in bacterial electron transfer chains or are of unknown function. The copper ion is solely bound by the protein matrix. A special distorted trigonal planar arrangement to two histidine and one cysteine ligands around the copper gives rise to very peculiar electronic properties of the metal site and an intense blue color. A number of cupredoxins have been crystallographically characterized at medium to high resolution. The cupredoxins in general have a low sequence homology but high structural homology. Gough & Clothia, Structure 12:917-925 (2004); De Rienzo et al. Protein Science 9: 1439-1454 (2000). For example, the amino acid sequence of azurirt is 31% identical to that of auracyamn B. 16.3% to that of rustic} anin, 20.3 % to that of plastoc\anm, and 17.3% to that of pseudoazurin. See, Table 1. However, the structural similarity of these proteins is more pronounced. The VAST p value for the comparison of the structure of azurin to auracyanin B is 10"' "\ azurin to rusticyanin is 10~s, azurin to plastocyanϊn is IG^6, and azurin to psuedoazurin is W4 \ All of the cupredoxins possess an eight-stranded Greek key beta-barrel or beta- sandwich fold and have a highly conserved site architecture, De Rienzo et at., Protein Science 9: 1439-1454 (2000), A prominent hydrophobic patch, due to the presence of many long chain aliphatic residues such as methionines and leucines, is present around the copper site in azυrins, amicyanins, cyanobacterial plastocyanins, cucumber basic protein and to a lesser extent, pseudeazurm and eukaryotic plastocyanins. Id. Hydrophobic patches are also found to a lesser extent in stellacyanin and rusticyanin copper sites, but have different features. Id.
Table 1. Sequence and structure alignment of azurin (UZG) from P. aeruginosa to other proteins using VAST algorithm.
PDB Align % P Sc RM Descrip ment length1 a a -value2 ore3 SD' tion identity
IAO 82 1 1 12. 1.9 Ascorba
Z A 2 8.3 O e-7 te oxidase
I QH 113 3 1 12. 1.9 Auracya
Q^A 1 Oe-7.4 ninB
1V54 79 2 1 11. 2.1 Cytocro
B l 0.3 Oe-6.0 me c oxidase
IGY 92 1 1 11. 1.8 Rusticy
2 A 6.3 0e-5.0 anin
3MS 74 8 1 10. 2.5 Motile
P A .1 Oe-6.7 Major Sperm
Protein5 liuz 74 2 1 10. 2.3 Plastocy
0.3 Oe-5.6 anin
IKG 90 5 1 10. 3.4 Ephrinb
Y E .6 Oe-4.6 2
IPM 75 1 1 9.8 2.3 Pseudoa
Y 7.3 0e-4.1 zuπn
'Aligned Length: The number of equivalent pairs of C-alpha atoms superimposed between the two structures, i.e. how many residues have been used to calculate the 3D superposition.
"P-VAL: The VAST p value is a measure of the significance of the comparison, expressed as a probability. For example, if the p value is 0.00 L then the odds are 1000 to 1 against seeing a match of this quality by pure chance. The p value from VAST is adjusted for the effects of multiple comparisons using the assumption that there arc 500 independent and unrelated t>pes of domains in the MMDB database. The p value shown thus corresponds to the p value for the pairwise comparison of each domain pair, divided by 500.
JScore: The VAST structure-similarity score. This number is related to the number of secondary structure elements superimposed and the quality of that superposition. Higher VAST scores correlate with higher similarity,
4RMSD: The root mean square superposition residual in Angstroms. This number is calculated after optimal superposition of two structures, as the square root of the mean square distances between equivalent C-alpha atoms. Note that the RJVlSD value scales with the extent of the structural alignments and that this size must be taken into consideration when using RMSD as a descriptor of overall structural similarity.
5 C. elegans major sperm protein proved to be an ephrin antagonist in ocyte maturation. Kuwabara, Genes and Development 17:155-161 (2003).
Azurin The azurins are copper containing proteins of 128 amino acid residues which belong to the family of cupredoxins involved in electron transfer in certain bacteria. The azurins include those from P. aeruginosa (PA) (SEQ ID NO: 1), A. xylosoxidans, and A. denitrificans. Murphy et ai, J. MoL Biol. 315:859-871 (2002). The amino acid sequence identity between the azurins varies between 60-90%, these proteins showed a strong structural homology. All azurins have a characteristic β-sandwich with Greek key motif and the single copper atom is always placed at the same region of the protein. In addition, azurins possess an essentially neutral hydrophobic patch surrounding the copper site. Id.
PIastocyanins The plastocyanins are soluble proteins of cyanobacteria, algae and plants that contain one molecule of copper per molecule and are blue in their oxidized form. They occur in the ehtorαplast where they function as electron carriers. Since the determination of the structure of poplar plastocyanin in 1978, the structure of algal (Scenedesmus, Enteromorpha, Chlamydomonas) and plant {French bean) plastocyanms has been determined either by crystal Iographic or NMR methods, and the poplar structure has been refined to 1,33 A resolution. SEQ ID NO: 3 shows the amino acid sequence of plastocyanin from Phormidium laminosum.. a thermophilic cyanobactcrium. Another plastocyanin of interest is from Viva pertussis. Despite the sequence divergence among plastocyanins of algae and vascular plants (e.g., 62% sequence identity between the Chlamydomonas and poplar proteins), the three- dimensional structures are conserved (e.g., 0.76 A rms deviation in the C alpha positions between the Chlamydomonas and Poplar proteins). Structural features include a distorted tetrahedral copper binding site at one end of an eight- stranded antiparallel beta-barrel, a pronounced negative patch, and a flat hydrophobic surface. The copper site is optimized for its electron transfer function, and the negative and hydrophobic patches are proposed to be involved in recognition of physiological reaction partners. Chemical modification, cross- linking, and site-directed mutagenesis experiments have confirmed the importance of the negative and hydrophobic patches in binding interactions with cytochrome f , and validated the model of two functionally significant electron transfer paths involving plastocyanin. One putative electron transfer path is relatively short (approximately 4 A) and involves the solvent-exposed copper ligand His-87 in the hydrophobic patch, while the other is more lengthy (approximately 12-15 A) and involves the nearly conserved residue Tyr-83 in the negative patch. Redinbo et at, J. Bioenerg. Biomembr. 26:49-66 (1994).
Rustkyaniπs
Rusticyanins are blue-copper containing single-chain polypeptides obtained from a Thiobacilhts (now called Acidithiobacillus). The X-ray crystal structure of the oxidized form of the extremely stable and highly oxidizing cupredoxin rusticyanin from Thiobacillus ferrooxidans (SEQ ID NO: 4) has been determined by multiwavelength anomalous diffraction and refined to 1.9 A resolution. The rusticyanins are composed of a core beta- sandwich fold composed of a six- and a seven-stranded b-sheet. Like other cupredoxins, the copper ion is coordinated by a cluster of four conserved residues (His 85, Cysl38. Hisl43, Met 148) arranged in a distorted tetrahedron. Walter, RX. et at. J. MoI. Biol. 263:730-51 (1996).
Pseudoazurins
The pseudoazurins are a family of blue-copper containing single-chain polypeptide. The amino acid sequence of pseudoazurin obtained from Achromobacter cyctoclastes is shown in SEQ ID XO: 5. The X-ray structure analysis of pseudoazurin stums that it has a similar structure to the a/unns although there i^ low sequence homology between these proteins. Two main differences exist between the overall structure of the pseudoazurins and azurins. There is a carboxy terminus extension in the pseudoazurins, relative to the azurins, consisting of two alpha-helices, hi the mid-peptide region azurins contain an extended ioop, shortened in the pseudoazurins, which forms a flap containing a short α-helix. The only major differences at the copper atom site are the conformation of the MET side-chain and the Met-S copper bond length, which is significantly shorter in pseudoazurin than in azurin.
Phytocyanins
The proteins identifiable as phytocyanins include, but are not limited to, cucumber basic protein, stellacyanin, mavicyanin, umecyanin, a cucumber peeling cupredoxin, a putative blue copper protein in pea pods, and a blue copper protein from Arabidopsis thalϊana. hi all except cucumber basic protein and the pea-pod protein, the axial methionine ligand normally found at blue copper sites is replaced by glutamine.
Auracyanin
Three small blue copper proteins designated auracyanin A. auracyanin B-I, and auracyanin B-2 have been isolated from the thermophilic green gliding photosynthetic bacterium Chloroflexus aurantiacus. The two B forms are glycoproteins and have almost identical properties to each other, but are distinct from the A form. The sodium dodecyl sulfate-polyacryl amide gel electrophoresis demonstrates apparent monomer molecular masses as 14 (A), 18 (B-2). and 22 (B-I) kDa.
The amino acid sequence of auracyanin A has been determined and showed auracyanin A to be a polypeptide of 139 residues. Van Dreissehe ct al, Protein Science 8:947-957 (1999). His58, Cysl23. Hisl28, and Metl 32 are spaced in a way to be expected if they are the evolutionary conserved metal Iigands as in the known small copper proteins plastocyanm and azurin. Secondary structure prediction also indicates that auracyanin has a general beta-barrel structure similar to thai of azurin from Pseudomonas aeruginosa and plastocyariin from poplar leaves. However, auracyanin appears to have sequence characteristics of both small copper protein sequence classes. The overall similarity with a consensus sequence of azurin is roughly the same as that with a consensus sequence of plastoeyanin, namely 30 5%. The N -terminal sequence region I - 18 of auracyanin is remarkably nch in glycine and hydroxy ammo acids. Id. Se^ exemplary amino acid sequence SEQ ID NO: 15 for chain A of auracyanin from Chloroflexus aurantiaciis (NCBI Protein Data Bank Accession No. AAM 12874).
The auracyanin B molecule has a standard cupredoxin fold. The crystal structure of auracyanin B from Chloroflexus aurantiacus has been studied. Bond et al, J. MoI. Biol. 306:47-67 (2001). With the exception of an additional N-terminal strand, the molecule is very similar to that of the bacterial cupredoxin, azurin. As in other cupredoxins. one of the Cu iigands lies on strand 4 of the polypeptide, and the other three lie along a large loop between strands 7 and 8. The Cu site geometry is discussed with reference to the amino acid spacing between the latter three Iigands. The crystallographically characterized Cu-binding domain of auracyanin B is probably tethered to the periplasmic side of the cytoplasmic membrane by an N-terminal tail that exhibits significant sequence identity with known tethers in several other membrane-associated electron-transfer proteins. The amino acid sequences of the B forms are presented in McManus et al. J. Biol. Chem. 267:6531-6540 (1992). See exemplary amino acid sequence SEQ ID NO: 16 for chain B of auracyanin from Chloroflexus aurantiacus (NCBI Protein Data Bank Accession No. IQHQA).
StelJacyanin
Stellacyanins are a subclass of phytocyanins, a ubiquitous family of plant cupredoxins. An exemplary sequence of a stellacyanin is included herein as SEQ ID NO: 14. The crystal structure of umecyanm, a stellacyanin from horseradish root (Koch et al, J. Am. Chem. Soc. 127:158-166 (2005)) and cucumber stellacyanin (Hart el al. Protein Science 5:2175-2183 (1996)) is also known. The protein has an overall fold similar to the other phytocyanins. The ephrin B2 protein ectodomain tertiary structure bears a significant similarity to stellacyanin. Toth et al, Developmental CeU 1 :83-92 (2001). An exemplary amino acid sequence of a stellacyanin is found in the National Center for Biotechnology Information Protein Data Bank as Accession No. IJER, SEQ ID NO: 14.
Cucumber basic protein
An exemplary amino acid sequence from a cucumber basic protein is included herein as SEQ ID NO: 17, The crystal structure of the cucumber basic protein (CBP). a type 1 blue copper protein, has been refined at 1.8 A resolution. The molecule resembles other blue copper proteins in having a Greek key beta-barrel structure, except that the barrel is open on one side and is better described as a "beta-sandwich"' or "beta-taco". Guss et al, J. MoI. Biol. 262:686-705 (1996). The ephrinB2 protein ectodomian tertiary structure bears a high similarity (rms deviation 1.5A for the 50 α carbons) to the cucumber basic protein. Toth et al, Developmental Cell 1 :83-92 (2001). The Cu atom has the normal blue copper NNSS' co-ordination with bond lengths Cu-
N(His39) = 1.93 A, Cu-S(Cys79) = 2.16 A, Cu-N(His84) = 1.95 A, Cu-S(Met89) = 2.61 A. A disulphide link, (Cys52)-S-S-(Cys85), appears to play an important role in stabilizing the molecular structure. The polypeptide fold is typical of a sub-family of blue copper proteins (phytocyanins) as well as a non-metalloprotein, ragweed allergen Ra3, with which CBP has a high degree of sequence identity. The proteins currently identifiable as phytocyanins are CBP, stellacyanin, mavicyanin, umecyanin, a cucumber peeling cupredoxin, a putative blue copper protein in pea pods, and a blue copper protein from Arabidopsis thaliana. In all except CBP and the pea-pod protein, the axial methionine ligand normally found at blue copper sites is replaced by glutamine. An exemplary sequence for cucumber basic protein is found in NCBI Protein Data Bank Accession No. 2CBP, SEQ ID NO: 17.
Methods of Use
The invention provides methods to prevent de novo malignancies in otherwise healthy patients comprising administering to the patient at least one peptide that is a cupredoxin, or variant, derivative or structural equivalent thereof, as described above. Chemopreventive therapies are based on the hypothesis that the interruption of processes involved in cancergenesis will prevent the development of cancer. The cupredoxin Pseudomonas aeruginosa azurin and the truncated azurin peptide p28 are now known to inhibit the development of premalignant lesions, either by inhibiting the initial formation of premalignant lesions, or killing or inhibiting the growth of premalignant lesions that are present. It therefore contemplated that a cupredoxin. or variant, derivative or structural equivalent thereof, as described above, with the ability to inhibit the development of premalignant lesions, may be used in chemopreventive therapies in otherwise healthy patients. Such otherwise healthy patients are, in some embodiments, patients at a higher risk to develop cancer than those in the general population. Cancers that may be prevented by treatment with the compositions of the invention include, but are not limited to, melanoma, breast, pancreas, glioblastoma, astrocytoma, lung, colorectal, neck and head, bladder, prostate, skin, and cervical cancer. In some embodiments, the patient may be human. In other embodiments, the patient is not human.
The invention further includes methods to study the development of cancer comprising contacting mammalian cells before or after induction with a carcinogen with a composition comprising cupredoxin, or a variant, derivative or structural equivalent thereof and observing the development of the cells. In some embodiments, the cells are mouse mammary gland cells, while in others they are other cells that may become malignant in mammals.
Patients at a higher at risk to develop cancer than the general population may be patients with high risk features, patients with premalignant lesions, and patients that have been cured of their initial cancer or definitively treated for their premalignant lesions. See generally Tsao et al, CA Cancer J Clin 54: 150-180 (2004). High risk features may be behavioral, genetic, environmental or physiological factors of the patient. Behavioral factors that predispose a patient to various forms of cancer include, but are not limited to, smoking, diet, alcohol consumption, hormone replacement therapy, higher body mass index, nulliparity, betal nut use, frequent mouthwash use, exposure to human papillomavirus, childhood and chronic sun exposure, early age of first intercourse, multiple sexual partners, and oral contraceptive use. Genetic factors that predispose a patient to various forms of cancer include, but are not limited to, a family history of cancer, gene carrier status of BRCAl and BRCA2, prior history of breast neoplasia, familial adenomatous polyposis (FAP), hereditary nonpolyposis colorectal cancer (HNPCC), red or blond hair and fair-skinned phenotype, xeroderma pigmentosum, and ethnicity. Environmental features that predispose a patient to various forms of cancer include, but are not limited to, exposure to radon, polycyclic aromatic hydrocarbons, nickel, chromate, arsenic, asbestos, chioromethyl ethers, benzo[a]pyrene. radiation, and aromatic amines from rubber or paint occupational exposure. Other miscellaneous factors that predispose a patient to various forms of cancer include, but are not limited to, chronic obstructive pulmonary disease with airflow obstruction, chronic bladder infections, schistosomiasis, older age. and immunocompromised status.
Additionally, patients at a higher risk of developing cancer may be determined by the use of various risk models that have been developed for certain kinds of cancer. For example, patients predisposed to breast cancer may be determined using the Gail risk model, orthe Claus model among others. See Gail et al . J Natl Cancer Inst 81 :1879- 1886 (1989); Cuzick, Breast 12:405-411 (2003); Huang et a!.. Am J Epidemiol 151:703-714 (2000).
Patients with premallgnant lesions are at a higher risk to develop cancer than the general population. The presence of premalignant lesions in or on a patient may be determined by many methods that are well known to those in the art. Intermediate markers or biomarkers that originate from premalignant lesions may be measured in a patient to determine if the patient harbors premalignant lesions. Chromosomal abnormalities occur in tumor cells and the adjacent histologicialiy normal tissues in the majority of cancer patients. Progression in chromosomal abnormalities parallels the phenotypic progression from premalignant lesion to invasive cancer. Thiberville et al, Cancer Res. 55:5133-5139 (1995). Therefore, chromosomal abnormalities associated with cancer may be used as intermediate markers to detect premalignant lesions in a patient. Common chromosomal abnormalities associated with cancer include, but are not limited to, allelic deletions or loss of heterozygosity (LOH) in tumor suppressor genes such as 3p (FHIT and others), 9p (9p21 for 17p {17pl3 for P53 gene and others) and I3q (13ql4 for retinoblastoma gene Rb and others). Deletions in 3p and 9p are associated with smoking and the early stages of lung cancer, Mao et al, J. Natl. Cancer Inst. 89:857-862 (1997). Deletions affecting 3p, 5q, 8p, 17p and 18q are common change in epithelial cancers. See generally Tsao et al, CA Clin. Cancer J. Clin. 54:153 (2004). Other chromosomal mutations associated with cancer include those which activate oncogenes. Oncogenes whose presence may be used as intermediate markers include, but are not limited to, Ras, c-myc, epidemral growth factor. erb-B2 and cyclins E, Dl and BL See generally id, at 154.
Other intermediate markers may be the products of genes up-regulated in premalignant cells and cancer cells. Genes that may be up-regulated in premalignant cells include, but are not limited to, eyelooxygenases COX-I and COX-2. telomerase. Other biomarkers of cancer cells, and some premalignant ceils, include, but are not limited to, p53, epidermal growth factor receptor (GFR). proliferating cell nuclear antigen (PCNA). RAS. COX-2, Ki-67, DNA aneuploidy. DNA polymerase-α, ER, Hetlneu. E-cadherin, RARβ, hTEKΪ, pi 6IS'K4a, FHIT (3pl4), Bcl-2, VEGF-R, HPV infection. LOH 9p21, LOH l?p, p- AKT, AwRNP A2/B1. RAF, Myc, c-KIT, cyclin Dl , E and BL IGFL bcl-2, pi 6. LOH 3p21 5, LOH 3p25. LOH 9p2L LOH 17pl3. LOH Bq., LOH φ. AMSH2, APC. DCC DPC4, JVlS. BAX. PSA, GSTPl , NF-kB. API . D3S2, HPV infection, LOH 3pl4. LOH 4q. LOH 5ρ, bladder tumor antigen (BTA), BTK TRAK (Alidex. Inc., Redmond WA), urinary tract matrix protein 22, fibrin degradation product, autodrine motility factor receptor, BCLA- 4, cytokeratin 20, hyaluronic acid, CYFRA 21 -1 , BCA, beta-human chorionic gonadotropin. and tissue polypeptide antigen (TPA). See generally id. at 155-157. Patients that have been cured of their initial cancers or have been definitively treated for their premalignant lesions are also at a higher risk to develop cancer than the general population. A second primary tumor refers to a new primary cancer in a person with a history of cancer. Second primary tumors are the leading cause of mortality in head and neck cancer. Id. at 150. A second primary tumor is distinct from a metastasis in that the former originates de novo while the later originates from an existing tumor. Patients that have been cured of cancer or premalignant lesions of the breast, head and neck, lung, and skin are at a particularly high risk to develop second primary tumors.
The compositions comprising a cupredoxin or variant, derivative or structural equivalent thereof can be administered to the patient by many routes and in many regimens that will be well known to those in the art. In specific embodiments, the cupredoxin, or variant, derivative or structural equivalent thereof is administered intravenously, intramuscularly, sub cutaneous iy, topically, orally, or by inhalation. The compositions may be administered to the patient by any means that delivers the peptides to the site in the patient that is at risk of developing cancer. In specific embodiments, the cupredoxin or variant. derivative or structural equivalent thereof is administered intraveneously.
In one embodiment, the methods may comprise co-administering to a patient one unit dose of a composition comprising a cupredoxin or a variant, derivative or structural equivalent of cupredoxin and one unit dose of a composition comprising another chemopreventive drug, in either order, administered at about the same time, or within about a given time following the administration of the other, for example, about one minute to about 6o minutes following the administration of the other drug, or about 1 hour to about 12 hours following the administration of the other drug. Chemopreventive drugs of interest include, but are not limited to, tamoxifen, aromatase inhibitors such as letrozoie and anastrozole (Arimidex*)- retinoids such as N-[4-hydroxyphenyl] retϊπamide (4-HPR, fenretinide), nonsteriodal antiinflammatory agents (NSAIDs) such as aspirin and sulindac, ceiecoxib (CGX-2 inhibitori defluoromethyiornithing (DFMO). ursodeoxycholic acid. 3-hvdroxy-3- methylglutaryl coenzyme A reductase inhibitors. EKI-785 (EGFR inhibitor). (antibody to VEGF-receptor), cetuximab (antibody to EGFR), retinoi such as vitamin A, beta-carotene, 13-cis retinoic acid, isotretinoin and retinyl palrmtate, α~tocopherolf interferon, oncolytic adenovirus dl!520 (ONYX-015). gefitinib, etretinate, finasteride, indole-3-carbinol, resveratrol, chlorogenic acid, raloxifene, and oltipraz.
Compositions for Facilitating Selective Entry of Compounds into Cancer Cells and Tumors
The present invention relates to methods and mateπals for delivering a cargo compound into a cell. Delivery of the cargo compound according to this invention is accomplished by the use of a suitable transport polypeptide. In one embodiment of the invention, the cargo compound is linked to the transport polypeptide. Suitable transport peptides include a cupredoxin, or a fragment of a cupredoxin containing a "cupredoxin entry domain". The term "cupredoxin entry domain" refers to a fragment of a cupredoxin that includes the amino sequence that is required for the entry of cupredoxin into a mammalian cancer cell. Cargo compounds delivered by the present invention include, but are not limited to, proteins, lipoproteins, polypeptides, peptides, polysaccharides, nucleic acids, including KNA, DNA and anti-sense nucleic acids, dyes, fluorescent and radioactive tags, microparticles or nanoparticles, toxins, inorganic and organic molecules, small molecules, and drugs (for example, chemopreventive drugs). In some embodiments, the drugs and toxins kill tumor cells.
In one embodiment of the invention, the cupredoxin is an azurin, such as azurin from Pseudomonas aeruginosa (SEQ ID NO: 1). In other embodiments of the invention, the cupredoxin is a plastocyanin, a rusticyanin, or a pseudoazuπn, among others. In specific embodiments, the azurin is from Pseudomonas aeruginosa, Pseudomonas syringa. Neisseria mcningitϊdes . Neisseria gonorrhoeae. Vibrio parahaemolyticus or Bordetclla bronchiseptica. among others.
In one embodiment, a cargo compound is delivered to kill or retard cell cycle progression in a cell, such as a cancer cell. Such a cancer cell can be, for example, an osteosarcoma cell, lung carcinoma cell, colon carcinoma cell, lymphoma cell. leukemia cell, soft tissue sarcoma cell or breast, liver, bladder or prostate carcinoma cell, among others. For example, the cargo compound can be a cell cycle control protein, such as p53; a cyclin- dependent kinase inhibitor, such as pi 6. p21 or p27, a suicide protein such as thymidine kinase or nitroreductase; a cytokine or other immunomodulatory protein such as interleukin 1 , interleukin 2 or granulocyte-macrophage colony stimulating factor (GM-CSF); or a toxin, such as Pseudomonas aeruginosa exotoxin A. among others. In other embodiments, a biologically active fragment of one of the above classes of compounds is delivered. In another embodiment, the cargo compound is delivered in order to generate an image of the target tissue. For example, the target tissue can be a cancer and the cargo compound can be one commonly used to generate an image for detection by X-ray computed tomography (CT), Magnetic Resonance Imaging (MRI) and ultrasound. In these embodiments, the cargo compound is a gamma ray or positron emitting radioisotope, a magnetic resonance imaging contrast agent, an X-ray contrast agent, or an ultrasound contrast agent.
The invention further includes methods of selectively introducing DNA or RNA into a mammalian cancer cell. In such embodiments, the DNA or RNA is the cargo compound. In some embodiments, the method includes providing pi 8 coupled to DNA or RNA and introducing the compound into the body of a mammal. In some embodiments, the DNA or RNA is a gene or a fragment of a gene. In some embodiments, the DNA or RNA has a therapeutic effect once introduced into a mammalian cell. Cupredoxin Entry Domain
The invention provides for a protein transduction domain that allows for the transport of linked cargo into mammalian cancer cells but not non-cancerous cells. It has been discovered that cupredoxin proteins comprise a protein transduction domain, the cupredoxin entry domain, which facilitates the entry of linked cargo into mammalian cancer cells. In some embodiments, the entire cupredoxin protein can be used to facilitate the transport linked cargo selectively into cancer cells. In other embodiments, a portion of a cupredoxin can be used to transport linked cargo into cancer cells. In some embodiments, the cupredoxin entry domain consists of a region of a cupredoxin that is less that the full length wild-type protein. In some embodiments, the cupredoxin entry domain consists more than about 10 residues, about 15 residues or about 20 residues of a cupredoxin. In some embodiments, the cupredoxin entry domain consists of not more than about 50 residues, about 40 residues or about 30 residues of a cupredoxin. In some embodiments, the cupredoxin entry domain has at least about 90% amino acid sequence identity, at least about 95% amino acid sequence identity or at least about 99° ό amino acid sequence identity to a cupredoxin. In some embodiments, the cupredoxm entry domain is a azitrin entry domain. In one embodiment of the present invention, aazurin entry domain contains at least amino acids 50 to 77 of ' Pseudomonas aeruginosa azurm (SEQ ID NO: 2). In another embodiment of the invention, the cupredoxin entry domain contains at least amino acids 36 to 7" of Pseudomonas aeruginosa azurin (SEQ ID NO: 27). In another embodiment of the invention, the cupredoxin entry domain contains at least ammo acids 36 to 89 of Pseudomonas aeruginosa azurin (SEQ ID NO: 28). In another embodiment of the invention, the cupredoxin entry domain contains at least ammo acids 36 to 128 of Pseudomonas aeruginosa azurin (SEQ ID NO: 29). In yet another embodiment of the invention, the cupredoxin entry domain contains at least amino acids 50 to 67 of Pseudomonas aeruginosa azurin (SEQ ID NO: 25). In another embodiment of the invention, the cupredoxin entry domain contains at least amino acids 53 to 70 of Pseudomonas aeruginosa azurin (SEQ ID NO: 30). In yet another embodiment of the invention, the cupredoxin entry domain contains at least amino acids 53 to 64 of Pseudomonas aeruginosa azurin (SEQ ID NO: 31). In another embodiment of the invention, the cupredoxin entry domain is an entry domain from a cupredoxin other than P. aeruginosa azurin. In different embodiments, the cupredoxin entry domain maybe a fragment of plastocyanin from the cyanobacteriurn Phormidium laminosum (SEQ ID NO: 3), rusticyanin from Thiobacillus ferrooxidans (SEQ ID NO: 4); pseudoazurin from Achromobacter cycloclastes (SEQ ID NO: 5), azurin from Pseudomonas syringae (SEQ ID NO: 21), azurin from Neisseria meningitidis (SEQ ID NO: 10), azurin from Vibrio parahaemolyticus (SEQ ID NO: 8), or an auracyanin from Chloroflexus aurantiacus (SEQ ID NO: 15 and 16).
In another embodiment of the invention, the cupredoxin entry domain contains at least amino acids 57 to 89 of auracyanin B of Chloroflexus aurantiacus (SEQ ID NO: 20). In another embodiment of the invention, the cupredoxm entrv domain contains at least ammo acids 51 -77 of Pseudomonas syringae azurm (S EQ ID NO: 21 ). In another embodiment of the invention, the cupredoxin entry domain contains at least amino acids 89-1 15 of Neisseria meningitidis hά''L (SEQ ID NO: 22). In another embodiment of the invention, the cupredoxin entry domain contains at least amino acids 52-78 of Vibrio parahaemolyticus azurin (SEQ ID NO: 23). In another embodiment of the invention, the cupredoxm entry domain contains at least ammo acids 51 -77 of Bordelella bronchiscpnca azurin (SEQ ID NO: 24). Modification of a Cupredoxin Entry Domain
In another embodiment of the present invention, a cupredoxin entry domain is chemically modified or genetically attered to produce variants that retain the ability to transport a cargo compound into a cell. For example, Example 14 shows that Pseudomonas aeruginosa azurin having proline residues introduced at positions 54, 61 and 70 retains its ability to enter UISO-Mel-2 cells.
In another embodiment, the cupredoxin entry domain comprises a conserved amino acid sequence DGXXXXXDXXYXKXXD (SEQ ID NO: 32) or DGXXXXDXXYXKXXD (SEQ ID NO: 33) where D is aspartic acid, G is glycine, Y is tyrosine, K is lysine and X is any amino acid. See Example 17.
Variants of a cupredoxin entry domain may be synthesized by standard techniques. Derivatives are amino acid sequences formed from native compounds either directly or by modification or partial substitution. Analogs are amino acid sequences that have a structure similar, but not identical, to the native compound but differ from it in respect to certain components or side chains. Analogs may be synthesized or from a different evolutionary origin.
Variants may be full length or other than full length, if the derivative or analog contains a modified amino acid. Variants of a cupredoxin entry domain include, but are not limited to, molecules comprising regions that are substantially homologous to the cupredoxin entry domain by at least about 65%, 70%, 75%. 85%, 90%. 95%, 98%, or 99% identity over an amino acid sequence of identical size or when compared to an aligned sequence in which the alignment is performed by a homology algorithm.
In another embodiment, the variants of a cupredoxin entry domain have a significant structural similarity to P, aeruginosa azurin residues 50-77 (SEQ ID NO: 2). In other embodiments, the variants of a cupredoxin entry domain have a significant structural similarity to P. aeruginosa azurin residues 50-67 (SEQ ID NO: 25). Examples of studies that determine significant structural homology between cupredoxins and other proteins include Toth c( al. (Developmental Cell 1:82-92 (2001)). Specifically, significant structural homology between a variant of the cupredoxin entry domain and P. aeruginosa azurin residues 50-^7 (SEQ ID NO: 2) is determined by using the VAST algorithm (Gibrat el al, Curr Opin Struct Bio! 6:3~7-385 (1996): Madej ex al , Proteins 23:356-3690 (1995)), In specific embodiments, the VAST p value from a structural comparison of a \ anant of the cupredoxm entry domain and P, aeruginosa azurin residues 50-77 (SEQ ID NO: 2) is less than about IG"3, less than about 10"5, or less than about IG7. in other embodiments, significant structural homology between a variant of the cupredoxin entry domain and P. aeruginosa azurin residues 50-77 (SEQ ID NO: 2) can be determined by using the DALl algorithm (Holm & Sander, J MoL Biol. 233:123-138 (1993)). ϊn specific embodiments, the DALI Z score for a pairwise structural comparison is at least about 3.5, at least about 7.0, or at least about 10.0.
Modifications to the cupredoxm entry domain can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis (Carter, Biochem J. 237: 1-7 (1986); Zoller and Smith, Methods Enzymol. 154:329-50 (1987)), cassette mutagenesis, restriction selection mutagenesis (Wells et α/., Gene 34:315-23 (1985)) or other known techniques can be performed on the cloned DNA to produce a cupredoxin entry domain variant nucleic acid. In addition, nucleotides encoding entry domains with structural similarity to that of the cupredoxin entry domains may be synthesized by methods that are well known in the art. Further, protein molecules that are wild type or variant cupredoxin entry domains may be synthesized by methods that are well known in the art.
Nucleic Acids Coding for a the Cupredoxin Entry Domain and Complex of a Cupredoxin Entry Domain Linked to a Cargo Compound
In another aspect, the present invention provides a nucleic acid molecule encoding a fusion protein comprising a cupredoxin entry domain linked to a cargo compound, where the cargo compound is a protein or peptide. The nucleic acid molecule according to the invention can be prepared by a combination of known techniques in the art. For instance. nucleic acid sequences for the cupredoxin entry domain and the cargo compound can individually be prepared by chemical synthesis or cloning. The nucleic acid sequences are then hgated in order with a Iigase to give a nucleic acid molecule of interest.
Methods of Delivering a Cargo Compound using a Cupredoxm Entry Domain Many arginine-rich peptides are known to translocate through mammalian ceil membranes and carry protein cargo compounds mside such cells. Suzuki. T., ct al. J. Biol. Chcm. 277:2437-43 (2002). For example, a short argimne-rich 1 1 ammo acid (ammo acids 47-57) segment of HIV Tat protein allows transport of cargo proteins into mammalian cells. Schwarze, SR., et al. Trends Cell Biol. 10:290-95 (2000). Synthetic entry domains that strengthen the alpha-helical content and optimize the placement of arginine residues have been shown to have enhanced potential as protein transduction domains. Ho. A., et al, Cancer Res. 61 :474-77 (2001). In comparison. P. aeruginosa azurin has a single arginine residue. It is therefore believed, but not relied upon for the present invention, that its mode of entry is different from that of the Tat protein.
The present invention encompasses the use of those cupredoxϊn fragments that facilitate the entry* of a cargo compound into a cell. Such fragments may be determined by any method that identifies those fragments required for entry into a cell. In one such method, a cupredoxin fragment is linked to a marker substance and a test performed to determine whether the cupredoxin fragment enters a cell. Such methods may be used to identify suitable fragments of the cupredoxins discussed above.
In various embodiments of the present invention, the cargo compound is attached to a cupredoxin or a fragment thereof, such as azurin from P. aeruginosa (SEQ ID NO: 1); plastocyanin from the cyanobacterium Phormidium laminosum (SEQ ID NO: 3); rusticyanin from Thiobaciilus ferrooxidans (SEQ ID NO: 4); or pseudoazurin from Achromobacter cycloclastes (SEQ ID NO: 5), a fragment of an azurin, from Pseudomonas syringae (SEQ ID XO: 21), azurin from Neisseria meningitidis (SEQ ID NO: 10), azurin from Vibrio parahaemofyticus (SEQ ID NO: 19), azurin from Bordetella bronchiseptica (SEQ ID NO: 8), auracyanin A and B from Chloroflexus aurantiacus (SEQ ID NO. 15 and 16), among other azurin and azurin-Hke proteins. In other embodiments, the cargo is linked to a cupredoxin entry domain such as p28 (SEQ ID NO: 2) or pi 8 (SEQ ID NO: 25).
In vaπous embodiments of the present invention, a cupredoxin entry domain delivers a cargo compound into a ceil in vitro, ex vivo or in iivo. For example, delivery may be achieved in vitro by adding a complex of a cupredoxin entrj, domain and a cargo compound to a cell culture, such as a pap smear. Alternatively, delivery may be achieved ex iivo by adding the complex to a sample removed from a patient, for example, blood, tissue, or bone marrow, and returning the treated sample to the patient. Delivery may also be achieved by administration of the complex directly to a patient. The methods of the present invention may be used for therapeutic, prophylactic, diagnostic or research purposes. Cargo compounds delivered by the present invention include, but are not limited to, proteins. lipoproteins, polypeptides, peptides, polysaccharides, nucleic acids, including anti-sense nucleic acids, dyes, microparticles or nanoparticles, toxins, organic and inorganic molecules, small molecules, and drugs.
In one embodiment, a detectable substance, for example, a fluorescent substance, such as green fluorescent protein; a luminescent substance; an enzyme, such as β-galactosidase; or a radiolabeled or biotinylated protein is delivered to confer a detectable phenotype to a cell. Similarly, microparticles or nanoparticles labeled with a detectable substance, for example, a fluorescent substance, can be delivered. One example of suitable nanoparticles is found in U.S. Pat. No. 6,383,500, issued May 7, 2002, which is hereby expressly incorporated by reference. Many such detectable substances are known to those skilled in the art.
In some embodiments, the cargo compound is a detectable substance that is suitable for X-ray computed tomography, magnetic resonance imaging, ultrasound imaging or radionuclide scintigraphy. In these embodiments, the cargo compound is administered to the patient for purposes of diagnosis. A contrast agent is administered as a cargo compound to enhance the image obtained by X-ray CT, MRI and ultrasound. The administration of a radionuclide cargo compound that is targeted to tumor tissue via the cupredoxin entry domain can be used for radionuclide scintigraphy. In some embodiments, the cupredoxin entry domain may contain the radionucleotide with or without a cargo compound. In other embodiments, the cargo compound is a gamma ray or positron emitting radioisotope, a magnetic resonance imaging contract agent, an X-ray contrast agent, or an ultrasound contrast agent.
Ultrasound contrast agents suitable for use as cargo compounds include, but are not limited to, a microbubble of a biocompatible gas, a liquid carrier, and a surfactant microsphere, further comprising an optional linking moiety, Un, between the targeting moieties and the microbubble. In this context, the term liquid carrier means aqueous solution and the term surfactant means any amphiphilic materia] which produces a reduction in interfacial tension in a solution, A list of suitable surfactants for forming surfactant microspheres is disclosed in EP0727225A2, herein expressly incorporated by reference. The term surfactant microsphere includes nanospheres, liposomes, vesicles and the like. The biocompatible gas can be air, or a fluorocarbon, such as a CJ-CJ perfluoroalkane, which provides the difference in echogenicity and thus the contrast in ultrasound imaging. The gas is encapsulated or contained in the microsphere to which is attached the cupredoxin entry domain, optionally via a linking group. The attachment can be covalent, ionic or by van der Waals forces. Specific examples of such contrast agents include lipid encapsulated perfluorocarbons with a plurality of tumor neovascuiature receptor binding peptides, polypeptides or peptidomimetics. X-ray contrast agents suitable for use as cargo compounds include, but are not limited to, one or more X-ray absorbing or "heavy" atoms of atomic number 20 or greater, further comprising an optional linking moiety. Ln, between the cupredoxin entry domain and the X- ray absorbing atoms. The frequently used heavy atom in X-ray contrast agents is iodine. Recently, X-ray contrast agents comprised of metal chelates (e.g., U.S. Pat. No. 5,417.959) and polychelates comprised of a plurality of metal ions (e.g., U.S. Pat. No. 5,679,810) have been disclosed. More recently, muitinuclear cluster complexes have been disclosed as X-ray contrast agents (e.g., U.S. Pat No. 5,804,161 , PCT WO91/14460, and PCT WO 92/17215). MRI contrast agents suitable for use as cargo compounds include, but are not limited to, one or more paramagnetic metal ions, further comprising an optional linking moiety, Ln, between the cupredoxin entry domain and the paramagnetic metal ions. The paramagnetic metal ions are present in the form of metal complexes or metal oxide particles. U.S. Pat. Nos. 5,412,148, and 5,760,191, describe examples of chelators for paramagnetic metal ions for use in MRI contrast agents. U.S. Pat. No. 5,801,228, U.S. Pat. No. 5,567,41 1 , and U.S. Pat. No. 5,281,704, describe examples of polychelants useful for complexing more than one paramagnetic metal ion for use in MRI contrast agents. U.S. Pat. No. 5,520,904, describes particulate compositions comprised of paramagnetic metal ions for use as MRI contrast agents.
In another embodiment, a cargo compound is delivered to kill or retard cell cycle progression in a cell, such as a cancer cell. Such a cancer cell can be, for example, an osteosarcoma cell, lung carcinoma cell, colon carcinoma cell, lymphoma cell, leukemia ceil, soft tissue sarcoma cell or breast, liver, bladder or prostate carcinoma cell. For example, the cargo compound can be a cell cycle control protein, such as p53; a cycl in-dependent kinase inhibitor, such as pi 6, p21 or p27; a suicide protein such as thymidine kinase or nitroreductase; a cytokine or other immunomodulatory protein such as interleukin 1. interleukin 2 or granulocyte-macrophage colony stimulating factor (GM-CSF); or a toxin, such as Pseudomonas aeruginosa exotoxin A. In other embodiments, a biologically active fragment of one of the above classes of compounds is delivered. In yet another embodiment, the cargo compound is a nucleic acid. In some embodiments the nucleic acid codes for one of the above classes of compounds. In yet another embodiment, the cargo compound is a drug used to treat cancer. Such drugs include, for example. 5-fluorouracil; Interferon α; Methotrexate; Tamoxifen; and Vincristine. The above examples are provided for illustration only, many other such compounds are known to those skilled in the art. In other embodiments, the nucleic acid is useful for gene therapy.
Cargo compounds suitable for treating cancer include, but not limited to. alkylating agents such as nitrogen mustards, alkyl sulfonates, nitrosoureas, ethyl enimines, and triazenes; antimetabolites such as folate antagonists, purine analogues, and pyrimidine analogues; antibiotics such as anthracyclines, bleomycins, mitomycin, dactinomycin, and plicamycin; enzymes such as L-asparaginase; farnesyl-protein transferase inhibitors; 5. alpha. -reductase inhibitors; inhibitors of 17.beta.-hydroxysteroid dehydrogenase type 3; hormonal agents such as glucocorticoids, estrogens/anti estrogens, androgens, antiandrogens, progestins, and luteinizing hormone-releasing hormone antagonists, octreotide acetate; microtubule-disruptor agents, such as ecteinascidins or their analogs and derivatives; microtubule-stabilizing agents such as taxanes, for example, paclitaxel (Taxol™)> docetaxel (Taxotere™), and their analogs, and epothilones, such as epothilones A-F and their analogs; plant-derived products, such as vinca alkaloids, epipodophyllotoxins, taxanes; and topiosomerase inhibitors; prenyl-protein transferase inhibitors; and miscellaneous agents such as hydroxyurea, procarbazine, mitotane, hexarnethylmelarnine, platinum coordination complexes such as cisplatin and carboplatin; and other agents used as anti-cancer and cytotoxic agents such as biological response modifiers, growth factors; immune modulators and monoclonal antibodies.
Representative examples of these classes of anti-cancer and cytotoxic agents include but are not limited to mechlorethamine hydrochloride, cyclophosphamide, chlorambucil, melphalan, ifosfamide. busuifan, carmustiϊi. lomustiπc, semustine. streptozociπ. thiotepa. dacarbazine. methotrexate, thioguanine. mercaptopurine, fludarahine, pentastatin, cladribin. eytarabine. fluorouracil, doxorubicin hydrochloride, daunorubicin, idarubicin, bleomycin sulfate, mitomycin C, actinomycin D, safracϊns, saframycins, quinocarcins, discodermolides. vincristine, vinblastine, vinorelbine tartrate, etoposide, etoposide phosphate, teniposide, paclitaxel. tamoxifen, estramustine, estramustme phosphate sodium, flutamide, buserelin. leuprohde. pfendϊnes. diynescs, arnisole, aflacon. interferon, mterleukms, aldesleukin. filgrastim, sargramostπn. rituximab. BCG. tretinoin, irinoteean hydrochloride, betamethosone, gemcitabine hydrochloride, altretamine. and topoteca and any analogs or derivatives thereof.
Preferred members of these classes include, but are not limited to, paclitaxel, cisplatin, carboplatin, doxorubicin, carminomycin, daunorubiein. aminopterin. methotrexate, methopterin, mitomycin C. ecteinascidin 743. or pofiromycin, 5-flυorouracil, 6- mercaptopurine. gemcitabine. cytosine arabinoside, podophyllotoxin or podophyllotoxin derivatives such as etoposide, etoposide phosphate or tenyposide, melphalan, vinblastine, vincristine, leurosidine, vindesine and leurosine.
Examples of anticancer and other cytotoxic agents useful as cargo compounds include the following: epothilone derivatives as found in German Patent No. 4138042.8; WO
97/19086, WO 98/22461 , WO 98/25929, WO 98/38192, WO 99/01124, WO 99/02224, WO 99/02514, WO 99-03848, WO 99/07692, WO 99/27890, WO 99/28324, WO 99/43653, WO 99/54330, WO 9954318, WO 99/54319. WO 99/65913, WO 99/67252, WO 99/67253 and WO 00/00485; cyclin dependent kinase inhibitors as found in WO 99/24416 (see also U.S. Pat. No. 6,040,321 ); and prenyl -protein transferase inhibitors as found in WO 9730992 and WO 98/54966; and agents such as those described generically and specifically in U.S. Pat. No. 6,011,029 (the compounds of which U.S. patent can be employed together with any NHR modulators (including, but not limited to, those of present invention) such as AR modulators, ER modulators, with LHRH modulators, or with surgical castration, especially in the treatment of cancer).
The above other therapeutic agents, when employed as cargo compounds with the compounds of the present invention, may be used, for example, in those amounts indicated in the Physicians' Desk Reference (PDR) or as otherwise determined by one of ordinary skill in the art.
Pharmaceutical Compositions Containing a Cupredoxin Entry Domain
Pharmaceutical compositions containing a complex of a cupredoxin entry domain linked to a cargo compound can be manufactured in any conventional manner, e.g., by conventional mixing, dissolving, granulating, dragee-making, emulsifying, encapsulating, entrapping, or lyophilizing processes. The complex can be readily combined with a pharmaceutically acceptable carrier well-known in the art. Such carriers enable the preparation to be formulated as a tablet, pill, dragee, capsule, liquid, gel, syrup, slurry, suspension, and the like. Suitable excipients can also include, for example, fillers and cellulose preparations. Other excipients can include, for example, flavoring agents, coloring agents, detackifiers. thickeners, and other acceptable additives, adjuvants, or binders.
Such compositions can be used in, for example, the detection or imaging of a cell type or in the treatment of a condition related to cell death or in the prevention thereof. The compositions can be administered in an amount sufficient to prevent or treat a condition related to resistance to cell death. As used herein, the term "a condition related to resistance to cell death" refers to a disease, state, or ailment characterized by at least a tendency for prolonged cell life when compared with a healthy cell of like kind as determined by a reasonable, skilled physician or clinician. Typically, the host organism is a mammal, such as a human or animal. Administration of Compositions Containing a Cupredoxin Entry Domain
Compositions containing a cupredoxin entry domain can be administered by any suitable route, for example, by oral, buccal, inhalation, sublingual, rectal, vaginal, transurethral, nasal, topical, percutaneous, i.e., transdermal or parenteral (including intravenous, intramuscular, subcutaneous and intracoronary administration). The compositions and pharmaceutical formulations thereof can be administered in any amount effective to achieve its intended purpose. When administrated to treat a condition related to resistance to cell death, the composition is administered in a therapeutically effective amount. A "therapeutically effective amount"' is an amount effective to prevent development of. or to alleviate the existing symptoms of, the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art. The appropriate dosage will, of course, vary depending upon, for example, the compound containing the cuprcdoxm entry domain employed, the host, the mode of administration and the nature and seventy of the conditions being treated or diagnosed. However, in one embodiment of the methods of the present invention, satisfactory treatment results in humans are indicated to be obtained at daily dosages from about 0.001 to about 20 mg/kg of body weight of the compound containing the cupredoxin entry domain. In one embodiment, an indicated daily dosage for treatment in humans may be in the range from about 0.7 mg to about 1400 mg of a compound containing the cupredoxin entry domain conveniently administered, for example, in daily doses, weekly doses, monthly doses, and or continuous dosing. Daily doses can be in discrete dosages from 1 to 12 times per day. Alternatively, doses can be administered every other day, every third day, fourth day, every fifth day, every sixth day. every week, and similarly in day increments up to 31 days. Dosing can be continuous, intermittent or a single dose, using any applicable dosing form, including tablet, patches, i.v. administration and the like. More specifically, the composition is administered in a therapeutically effective amount. In specific embodiments, the therapeutically effective amount is from about 0.01-20 rng/"kg of body weight. In specific embodiments, the dose level is about 10 mg/lcg/day, about 15 rng/kg/day, about 20 mglcg/day, about 25 mg/kg/day, about 30 mg'kg'day, about 35 mg, leg/day, about 40 mg/kg/ day, about 45 mg/kg/day or about 50 mg'kg/day.
The method of introducing compounds containing the cupredoxin entry domain to patients is, in some embodiments, co-administration with other drugs known to treat cancer. Such methods are well-known in the art. In a specific embodiment, the compounds containing the cupredoxin entry domain are part of an cocktail or co-dosing containing or with other drugs for treating cancer. Such drugs include, for example, those listed herein and specifically 5-fluorouracil; Interferon α; Methotrexate; Tamoxifen; and Vincristine. The above examples are provided for illustration only, many other such compounds are known to those skilled in the art.
Nucleic acid molecules encoding a cupredoxin entry domain or a fusion protein combining a either entry domain and a cargo compound can be inserted into \ectors and used as gene therapy vectors. Gene therapy \ ectors can be delivered to a subject by, for example, intravenous injection, local administration (Nabel et al., U.S. Patent No. 5,328,470 1994. USA), or by stereotactic injection (Chen et ah. Proc Natl Acad Sci USA, vol. 91, pp 3054-57 ( 1994)) The pharmaceutical preparation of a gene therap) vector cars include an acceptable diluent or can comprise a slow release main K in which the gene ss imbedded Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells that produce the gene delivery system.
In one aspect, the composition is delivered as DNA such that the complex is generated in situ. In one embodiment, the DNA is '"naked," as described, for example, in Ulmer ct al, Science 259:1745-49 (1993) and reviewed by Cohen, Science 259 1691-92 (1993). The uptake of naked DNA may be increased by coating the DNA onto a carrier, e.g. a biodegradable bead, which is efficiently transported into the cells. In such methods, the DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, bacterial and viral expression systems. Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art. See, e.g., WO90/1 1092, WO93/24640, WO 93/17706, and U.S. Pat. No. 5,736,524.
Vectors, used to shuttle genetic material from organism to organism, can be divided into two general classes: Cloning vectors are replicating plasmid or phage with regions that are non-essential for propagation in an appropriate host cell and into which foreign DNA can be inserted; the foreign DNA is replicated and propagated as if it were a component of the vector. An expression vector (such as a plasmid, yeast, or animal virus genome) is used to introduce foreign genetic material into a host cell or tissue in order to transcribe and translate the foreign DNA, such as the DNA of the composition. In expression vectors, the introduced DNA is operably-linked to elements such as promoters that signal to the host cell to transcribe the inserted DNA Some promoters are exceptionally useful, such as inducible promoters that control gene transcription in response to specific factors. Operably-linking a composition polynucleotide to an inducible promoter can control the expression of the wt- azurin entry domain composition polypeptide or fragments. Examples of classic inducible promoters include those that are responsive to α-interferon, heat shock, heavy metal ions, and steroids such as glucocorticoids (Kaufman, Methods Enzymol. 185:487-51 1 (1990)) and tetracycline. Other desirable inducible promoters include those that are not endogenous to the cells in which the construct is being introduced, but. however, are responsive in those cells when the induction agent is exogenously supplied. In general, useful expression vectors are often plasm ids. However, other forms of expression vectors, such as viral vectors (e &.., replication defective retroviruses, adenoviruses and adeno-associated viruses) are contemplated.
Vector choice is dictated by the organism or cells being used and the desired fate of the vector. In general, vectors comprise signal sequences, origins of replication, marker genes, enhancer elements, promoters, and transcription termination sequences.
Kits Comprising a Cupredoxin Entry Domain-Cargo Compound Complex In another aspect, the invention provides kits containing one or more of the following in a package or container: (1) a reagent comprising a complex of a cupredoxin entry domain linked to a cargo compound; (2) a reagent containing a pharmaceutically acceptable adjuvant or excipient; (3) a vehicle for administration, such as a syringe; (4) instructions for administration. Embodiments in which two or more of components (1) - (4) are found in the same container are also contemplated.
Pharmaceutical Compositions Comprising Cupredoxin a Cupredoxin Entry Domain, a Cupredoxin Entry Domain - Cargo Compound Complex, Or Variant, Derivative Or Structural Equivalent Thereof
Pharmaceutical compositions comprising cupredoxin or variant, derivative or structural equivalents thereof, can be manufactured in any conventional manner, e.g., by conventional mixing, dissolving, granulating, dragee-making, emulsifying, encapsulating, entrapping, or lyophilizing processes. The substantially pure or pharmaceutical grade cupredoxin or variants, derivatives and structural equivalents thereof can be readily combined with a pharmaceutically acceptable carrier well-known in the art. Such carriers enable the preparation to be formulated as a tablet, pill, dragee, capsule, liquid, gel, syrup, slurry, suspension, and the like. Suitable carriers or excipierits can also include, for example, fillers and cellulose preparations. Other excipients can include, for example, flavoring agents, coloring agents, detackifiers, thickeners, and other acceptable additives, adjuvants, or binders. In some embodiments, the pharmaceutical preparation is substantially free of preservatives. In other embodiments, the pharmaceutical preparation may contain at least one preservative. General methodology on pharmaceutical dosage forms is found in Ansel et at, Pharmaceutical Dosage Forms and Drug Delivery Systems (Lippencott Williams & Wilkins. Baltimore MD (1999)). The composition comprising a cupredoxin or variant, derivative or structural equivalent thereof used in the invention may be administered in a variety of ways, including by injection (e.g.. intradermal, subcutaneous, intramuscular, intraperitoneal and the like), by inhalation, by topical administration, by suppository, by using a transdermal patch or by mouth. General information on drug delivery systems can be found in Ansel et ah, id., In some embodiments, the composition comprising a cupredoxin or variant, derivative or structural equivalent thereof can be formulated and used directly as injectibles, for subcutaneous and intravenous injection, among others. The injectable formulation, in particular, can advantageously be used to treat patients that are appropriate for chemopreventive therapy. The composition comprising a cupredoxin or variant, derivative or structural equivalent thereof can also be taken orally after mixing with protective agents such as polypropylene glycols or similar coating agents.
When administration is by injection, the cupredoxin or variant, derivative or structural equivalent thereof may be formulated in aqueous solutions, specifically in physiologically compatible buffers such as Hanks solution, Ringer's solution, or physiological saline buffer. The solution may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the cupredoxin or variant, derivative or structural equivalent thereof may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen- free water, before use. In some embodiments, the pharmaceutical composition does not comprise an adjuvant or any other substance added to enhance the immune response stimulated by the peptide. In some embodiments, the pharmaceutical composition comprises a substance that inhibits an immune response to the peptide.
When administration is by intravenous fluids, the intravenous fluids for use administering the cupredoxin or variant, derivative or structural equivalent thereof may be composed of crystalloids or colloids. Crystalloids as used herein are aqueous solutions of mineral salts or other water-soluble molecules. Colloids as used herein contain larger insoluble molecules, such as gelatin. Intravenous fluids may be steπle.
Crystalloid fluids that may be used for intravenous administration include but are not limited to. normal saline (a solution of sodium chloride at 0.9% concentration). Ringer's lactate or Ringer's solution, and a solution of 5% dextrose in water sometimes called D5W, as described in Table 2. Table 2. Composition of Common Crystalloid Solutions
Solution Other [NaI [CIl JGIucose] Name
D5W 5% 0 0 252 Dextrose
2 3 & 3.3% 51 51 168 1-3 Dextrose 0.3% saline
Half- 0.45% 77 77 0 normal saline NaCl
Normal 0.9% 154 154 0 saline NaCl
Ringer's Ringer's 130 109 0 lactate* solution
*Ringer's lactate also has 28 mmol/L lactate, 4 mmoL'L K' and 3 mmol/L Ca2÷.
When administration is by inhalation, the cupredoxin or variant, derivative or 5 structural equivalent thereof may be delivered in the form of an aerosol spray from pressurized packs or a nebulizer with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin, for use in an inhaler or0 insufflator may be formulated containing a powder mix of the proteins and a suitable powder base such as lactose or starch.
When administration is by topical administration, the cupredoxin or variant, derivative or structural equivalent thereof may be formulated as solutions, gels, ointments, creams, jellies, suspensions, and the like, as are well known in the art. In some embodiments,5 administration is by means of a transdermal patch. When administration is by suppository (eg , rectal or vaginal), cupredoxin or variants and derivatives thereof compositions may also be formulated in compositions containing conventional suppository bases.
When administration is oral, a cupredoxin or variant, derivative or structural equivalent thereof can be readily formulated by combining the cupredoxin or variant,t) derivative or structural equivalent thereof with pharmaceutically acceptable earners vteli known in the art, A solid carrier, such as mannitol, lactose, magnesium stearate, and the like may be employed; such carriers enable the cupredoxin and variants, derivatives or structural equivalent thereof to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a subject to be treated. For oral solid formulations such as, for example, powders, capsules and tablets, suitable excipients include fillers such as sugars, cellulose preparation, granulating agents, and binding agents.
Other convenient carriers, as well-known in the art, also include multivalent carriers, such as bacterial capsular polysaccharide, a dextran or a genetically engineered vector. In addition, sustained-release formulations that include a cupredoxin or variant, derivative or structural equivalent thereof allow for the release of cupredoxin or variant, derivative or structural equivalent thereof over extended periods of time, such that without the sustained release formulation, the cupredoxin or variant, derivative or structural equivalent thereof would be cleared from a subject's system, and/or degraded by, for example, proteases and simple hydrolysis before eliciting or enhancing a therapeutic effect. The half-life in the bloodstream of the peptides of the invention can be extended or optimized by several methods well known to those in the art. The peptide variants of the invention may include, but are not limited to, various variants that may increase their stability, specific activity, longevity in the bloodstream, and/or decrease immunogenicity of the cupredoxin, while retaining the ability of the peptide to inhibit the development of premalignant lesions in mammalian cells, tissues and animals. Such variants include, but are not limited to, those which decrease the hydrolysis of the peptide, decrease the deamidation of the peptide, decrease the oxidation, decrease the immunogenicity, increase the structural stability of the peptide or increase the size of the peptide. Such peptides also include circularized peptides (see Monk ct a!,, BioDrugs 19f4):261-78, (2005); DeFreest et ah. J. Pept. Res. 63(5):409~19 (2004)). DX-peptides (diastereomeri, Futaki et a!., j, Biol. Chem. Feb 23:276(8):5836-40 (2001 ); Papo a aL Cancer Res. 64(] ό):5779~8ό (2004); Miller et al., Biochem, Pharmacol. 36{ l):169-76, (19S"?)); peptides containing unusual amino acids (see Lee et al., J. Pept. Res. 63(2):69-84 (2004) j, N- and C- terminal modifications (see Labrie et al., Clin. Invest. Med. 13(5):275-8, (1990)), hydrocarbon stapling (see Schafineister et al . J. Am. Chem. Soc. 122:5891 -5892 (2000); Walcnski ct al.. Science 305: 1466-1470 (2004)) and PEG>lation. In various embodiments, the pharmaceutical composition includes carriers and excipients (including but not limited to buffers, carbohydrates, mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacteπostats. chelating agents, suspending agents, thickening agents and/or preservatives), water, oils, saline solutions, aqueous dextrose and glycerol solutions, other pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as buffering agents, tonicity adjusting agents, wetting agents and the like. It will be recognized that, while any suitable carrier known to those of ordinary skill in the art may be employed to administer the compositions of this invention, the type of carrier will vary depending on the mode of administration. Compounds may also be encapsulated within liposomes using well-known technology. Biodegradable microspheres may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Patent Nos. 4.897,268; 5,075,109; 5,928,647; 5,811 ,128; 5,820,883; 5,853,763; 5,814,344 and 5,942,252. The pharmaceutical compositions may be sterilized by conventional, well-known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyopbilized, the lyophilized preparation being combined with a sterile solution prior to administration.
Administration of Cupredoxin or Variant, Derivative or Structural Equivalent
Thereof
The cupredoxin or variant, derivative or structural equivalent thereof can be administered formulated as pharmaceutical compositions and administered by any suitable route, for example, by oral, buccal, inhalation, sublingual, rectal, vaginal, transurethral, nasal, topical, percutaneous, i.e., transdermal or parenteral (including intravenous, intramuscular, subcutaneous and intracoronary) or vitreous administration. The pharmaceutical formulations thereof can be administered in any amount effective to achieve its intended purpose. More specifically, the composition is administered in a therapeutically effective amount. In specific embodiments, the therapeutically effective amount is generally from about 0.01 -20 mg/day/kg of body weight.
The compounds comprising cupredoxin or \ ariant, derivathe or structural equivalent thereof are useful for the prevention of cancer, alone or in combination w. ith other active agents and ΌΓ cargo compounds. The appropriate dosage will, of course, vary depending upon, for example, the compound of cupredoxin or variant, derivative or structural equivalent thereof employed, the host, the mode of administration and the nature and severity of the potential cancer. However, in general, satisfactory results in humans are indicated to be obtained at daily dosages from about 0.01-20 mg/kg of body weight. An indicated daily dosage in humans is in the range from about 0.7 mg to about 1400 mg of a compound of cupredoxin or variant, derivative or structural equivalent thereof conveniently administered, for example, in daily doses, weekly doses, monthly doses, and'or continuous dosing. Daily doses can be in discrete dosages from 1 to 12 times per day. Alternatively, doses can be administered every other day. every third day, every fourth day, every fifth day, every sixth day, every week, and similarly in day increments up to 31 days or over. Alternatively, dosing can be continuous using patches, Lv. administration and the like.
The exact formulation, route of administration, and dosage is determined by the attending physician in view of the patient's condition. Dosage amount and interval can be adjusted individually to provide plasma levels of the active cupredoxin or variant, derivative or structural equivalent thereof, with or without a cargo compound, which are sufficient to maintain therapeutic effect. Generally, the desired cupredoxin or variant, derivative or structural equivalent thereof is administered in an admixture with a pharmaceutical carrier selected with regard to the intended route of administration and standard pharmaceutical practice.
In one aspect, the cupredoxin or variant, derivative or structural equivalent thereof is delivered as DNA such that the polypeptide is generated in situ. In one embodiment, the DNA is "naked." as described, for example, in Ulmer et aL (Science 259:1745-1749 (1993)) and reviewed by Cohen (Science 259:1691-1692 (1993)). The uptake of naked DNA may be increased by coating the DNA onto a carrier, e g,. biodegradable beads, which are then efficiently transported into the cells. In such methods, the DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, bacterial and viral expression systems. Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art. See, e.g., WO90/1 1092. WO93/24640, WO 93/17706. and U.S. Pat, No, 5,736,524. Vectors, used to shuttle genetic material from organism to organism, can be dhided into two general clashes' Cloning vectors are replicating plasmtd or phage with regions that are essential for propagation in an appropriate host cell and into which foreign DNA can be inserted; the foreign DNA is replicated and propagated as if it were a component of the vector. An expression vector (such as a plasmid, yeast, or animal virus genome) is used to introduce foreign genetic material into a host cell or tissue in order to transcribe and translate the foreign DNA, such as the DNA of a cupredoxin. In expression vectors, the introduced DNA is operably-linked to elements such as promoters that signal to the host cell to highly transcribe the inserted DNA. Some promoters are exceptionally useful, such as inducible promoters that control gene transcription in response to specific factors. Operably-linking a cupredoxin and variants and derivatives thereof polynucleotide to an inducible promoter can control the expression of the cupredoxin and variants and derivatives thereof in response to specific factors. Examples of classic inducible promoters include those that are responsive to α-interferon, heat shock, heavy metal ions, and steroids such as glucocorticoids (Kaufman, Methods Enzymol. 185:487-511 (1990)) and tetracycline. Other desirable inducible promoters include those that are not endogenous to the cells in which the construct is being introduced, but, are responsive in those cells when the induction agent is exogenously supplied. In general, useful expression vectors are often plasmids. However, other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses) are contemplated. In addition, the peptides of the present invention, including in one embodiment, pi 8, may be used as a vector to selectively deliver therapeutic compounds into cancer cells or tumors.
Vector choice is dictated by the organism or cells being used and the desired fate of the vector. In general, vectors comprise signal sequences, origins of replication, marker genes, polylinker sites, enhancer elements, promoters, and transcription termination sequences.
Kits Comprising Cupredoxin, or Variant, Derivative Or Structural Equivalent Thereof
In one aspect, the invention provides regimens or kits comprising one or more of the following in a package or container: (1 ) a pharmacologically active composition comprising at least one cupredoxin or variant, derivative or structural equivalent thereof; (2) an additional chemopreventive drag, (3; apparatus to administer the biologically active composition to the patient, such as a synnge. nebulizer etc.. When a kit is supplied, the different components of the composition may be packaged in separate containers, if appropriate, and admixed immediately before use. Such packaging of the components separately may permit long-term storage without losing the active components' functions, The reagents included in the kits can be supplied in containers of any sort such that the life of the different components are preserved and are not adsorbed or altered by the materials of the container. For example, sealed glass ampules may contain lyophilized cupredoxin and variants, derivatives and structural equivalents thereof , or buffers that have been packaged under a neutral, non-reacting gas, such as nitrogen. Ampules may consist of any suitable material, such as glass, organic polymers, such as polycarbonate, polystyrene, etc., ceramic, metal or any other material typically employed to hold similar reagents. Other examples of suitable containers include simple bottles that may be fabricated from similar substances as ampules, and envelopes, that may comprise foil-lined interiors, such as aluminum or an alloy. Other containers include test tubes, vials, flasks, bottles, syringes, or the like. Containers may have a sterile access port, such as a bottle having a stopper that can be pierced by a hypodermic injection needle. Other containers may have two compartments that are separated by a readily removable membrane that upon removal permits the components to be mixed. Removable membranes may be glass, plastic, rubber, etc.
Kits may also be supplied with instructional materials. Instructions may be printed on paper or other substrate, and/or may be supplied as an electronic-readable medium, such as a floppy disc, CD-ROM, DVD-ROM, Zip disc, videotape, audiotape, flash memory device etc. Detailed instructions may not be physically associated with the kit; instead, a user may be directed to an internet web site specified by the manufacturer or distributor of the kit, or supplied as electronic mail.
Modification of Cupredoxin, Cupredoxin Entry Domains and Variants, Derivatives and Structural Equivalents Thereof
Cupredoxin or variant, derivative or structural equivalents thereof may be chemically modified or genetically altered to produce variants and derivatives as explained above. Such variants and derivatives may be synthesized by standard techniques. Cupredoxin entry domains mav be similarly modified. In addition to naturally-occurring allelic variants of cupredoxin, changes can be introduced by mutation into cupredoxin coding sequence that incur alterations in the amino acid sequences of the encoded cupredoxin that do not significantly alter the ability of cupredoxin to inhibit the development of premalignant lesions. A "non-essential" amino acid residue is a residue that can be altered from the wild-type sequences of the cupredoxin without altering pharmacologic activity, whereas an "essential" amino acid residue is required for such pharmacologic activity. For example, ammo acid residues that are conserved among the cupredoxins are predicted to be particularly non-amenable to alteration, and thus "essential." Amino acids for which conservative substitutions that do not change the pharmacologic activity of the polypeptide can be made are well known in the art. Useful conservative substitutions are shown in Table 3, "Preferred substitutions," Conservative substitutions whereby an amino acid of one class is replaced with another amino acid of the same type fall within the scope of the invention so long as the substitution does not materially alter the pharmacologic activity of the compound.
Table 3. Preferred substitutions
Original Exemplary Preferred residue substitutions substitutions
AIa (A) VaI, Leu, He VaI
Arg (R) Lys, GIn, Asn Lys
Asn (K) GIn, His, Lys, Arg GIn
Asp (D) GIu GIu
Cys (C) Ser Ser
GIn (Q) Asn Asn
GIu (E) Asp Asp
GIy (G) Pro. Ala Ala
His (H) Asn. GIn. Lys. Arg Arg
Leu, VaL Met, Ala. Phe, lie (I) Leu
Norleucine
Norieucinc, lie, VaI,
Leu CL) He Met, Ala. Phe
Lys (K) Arg, GIn, Asn Arg
Met (M) Leu, Phe, He Leu
Phe (F) Leu, VaL He, Ala. Tyr Leu
Pro (P) Ala Ala
Ser (S) Thr Thr
Thr (T, Ser Ser Tyr (Y) Trp, Phe, Thr, Ser Phe
VaI (V) Ile' Lc,U' Met' Phe- Ala' Leu
Norleucme
Non-conservative substitutions that affect (1) the structure of the polypeptide backbone, such as a β~sheet or α-helical conformation, (2) the charge, (3) hydrophobicity, or (4) the bulk of the side chain of the target site can modify the pharmacologic activity. Residues are divided into groups based on common side-chain properties as denoted in Table 4. Non-conservative substitutions entail exchanging a member of one of these classes for another class. Substitutions may be introduced into conservative substitution sites or more specifically into non-conserved sites.
Table 4. Amino acid classes
Class Amino acids
Norleucine, Met, Ala, VaI, hydrophobic
Leu, lie neutral hydrophilic Cys, Ser, Thr acidic Asp, GIu basic Asn, GIn, His, Lys, Arg disrupt chain
GIy, Pro conformation aromatic Trp, Tyr, Phe
The variant polypeptides can be made using methods known in the art such as oligonucleotide-mediated (site-directed) mutagenesis, alanine scanning, and PCR mutagenesis. Site-directed mutagenesis (Carter, Biochem J. 237:1-7 (1986): Zollcr and Smith, Methods Enzymol. 154:329-350 (1987))» cassette mutagenesis, restriction selection mutagenesis (Wells ei aL, Gene 34:315-323 (1985)) or other known techniques can be performed on the cloned DNA to produce the cupredoxin variant DNA.
Known mutations of cupredoxins can also be used to create variant cupredoxin to be used in the methods of the invention. For example, the Cl 12D and M44KM64E mutants of ayutm are known to have cytotoxic and growth arresting activity that is different from the native azurin. and such altered activity can be useful in the treatment methods of the present invention.
A more complete understanding of the present invention can be obtained by reference to the following specific Examples. The Examples are described solely for purposes of illustration and are not intended to limit the scope of the invention. Changes in form and substitution of equivalents are contemplated as circumstances may suggest or render expedient. Although specific terms have been employed herein, such terms are intended in a descriptive sense and not for purposes of limitations. Modifications and variations of the invention as hereinbefore set forth can be made without departing from the spirit and scope thereof.
EXAMPLES
Example 1. Effect of peptide P-28 on DMBA-Induced Mammary lesions in the MMOC Model
The mouse mammalary gland organ culture (MMOC) model allows evaluating efficacy of potentially chemopreventive agents against development of mammary alveolar lesions (MAL) or mammary ductal lesions (MDL) in response to DMBA. DMBA under appropriate incubation conditions form either MAL or MDL based on the hormonal milieu in the medium. Hawthorne et al. , Pharmaceutical Biology 40: 70-74 (2002); Mehta et at. , J.
Natl. Cancer Inst. 93: 1103-1 106 (2001). Estrogen and progesterone-treated glands in culture develop ductal lesions whereas aldosterone and hydrocortisone- treated glands form estrogen and progesterone-independent alveolar lesions. Mammary glands not exposed to a carcinogen or chemopreventive agent, undergo structural regression in the absence of growth- promoting hormones, whereas treatment with DMBA for the 24-hr period between days 3 and 4 the regression of structures caused by deprivation of hormones. It is assumed that this is because the glands have lost normal hormonal responsiveness and now have altered their course of development. Generating mammary adenocarcinoma by transplanting transformed cells into syngeneic mice has proved the prernalignant preneoplastic nature of these unrepressed areas.
The thoracic pair of mammary glands was excised asepticaily from each BaJb-'c mouse, and the glands were divided into several groups. The effects of p2H were evaluated at 4 different dilutions in the medium. Carcinogen treated glands without the test agent served as a measure to determine percent incidence in the absence of a chemopreventive agent. An additional control was included to serve as a positive control for chemoprevention. Azurin was included in the medium at 50 μg/ml concentration. For alveolar lesions (MAL) stained glands were evaluated for the incidence of lesions (glands containing any lesions as compared to total number of glands in a given treatment group). For the ductal lesions (MDL) similar protocol was adapted, however, as indicated below in the methods section the hormonal combination is different for alveolar and ductal lesions. The glands were fixed in formalin and then processed for histopathology. The sections are stained with eosin and hematoxelene and evaluated under microscope. Here the multiplicity of ductal lesions between the control and the treatment groups are compared.
Organ Culture Procedure. The experimental animals used for the studies were young, virgin BALB/ c female mice 3 to 4 weeks of age obtained from Charles River, Wilmington, MA. The mice were treated daily by subcutaneous injections with 1 μg estradiol- 17β + 1 mg progesterone for 9 days. This treatment is a prerequisite inasmuch as animals not pretreated with steroids fail to respond to hormones in vitro. The entire culture procedure is described in detail. Jang et al, Science 275:218-220 (1997); Mehta, Eu. J. Cancer 36:1275-1282 (2000); Mehta et al, J. Natl. Cancer Inst. 89:212-219 (1997); Mehta et aL, J. Natl. Cancer Inst. 93:1103-1106 (2001). Briefly, the animals were killed by cervical dislocation, and the thoracic pair of mammary glands were dissected out on silk rafts and incubated for 10 days in serum free Waymouth MB752/ 1 medium (5-glands^5 ml/dish). The medium was supplemented with glutamine, antibiotics (penicillin and streptomycin 100 units/ ml medium) and growth - promoting hormones, 5 μg insulin (I), 5 μg prolactin (P), 1 μg aldosterone (A) and ϊ μg hydrocortisone (H) per ml of medium for the protocol to induce mammary alveolar lesions (MAL). For induction of ductal lesions (MDL), the medium contained 5 μg,ml, 5 μg/ml P. 0.001 μg/ml estradiol !7β and 1 μg/ml progesterone (Pg). Mehta et a!., J. Natl. Cancer Inst. 93:1 103-1 106 (2001). The carcinogen, DMBA (2 μgml) was added to the medium between days 3 and 4. For the present study, DMBA was dissolved in DMSO at a final concentration of 4 nig/ml, and 50 μg I was added to 100 ml medium resulting in 2 μg/ml final concentrations. The control dishes contained DMSO ΆS vehicle.
-f>4- On day 4. DMBA is removed from the medium by rinsing the glands in fresh medium and transferring them to new dishes containing fresh medium without DMBA. After 10 days of incubation, the glands were maintained for another 14 days in the medium containing only
I (5 μg'mi). During the entire culture period, the glands were maintained at 37°C under 95% Cb and 5% CO2 environment. The chemopreventive agent was included in the medium during the first ten days of growth -promoting phase. The test peptide p28 was evaluated at 4 concentrations ranging from 12.5 μg/ml to 100 μg/ml. Azurin was evaluated at 50 μgm! in the medium. The peptide was dissolved in sterile water and filtered prior to use. The medium was changed three times per week (Monday, Wednesday and Friday). At the end of the exposure, the glands were fixed in formalin.
Results were analyzed by Chi-square analysis and Fisher's Exact Test. Morphometic Analysis of MAL. For examination of MAL, the glands were stained in alum carmine, and evaluated for the presence of the lesions. The glands were scored for the presence or absence of mammary lesions, severity of lesions per gland, and toxicity of the agent. The glands stored in xylene were evaluated for the presence or absence, incidence, and severity of mammary lesions for each gland under a dissecting microscope. Mammary glands were scored as positive or negative for mammary lesions, and the percent incidence was determined as a ratio of glands exhibiting lesions and the total number of glands in that group. Dilation of ducts or disintegration of mammary structure because of treatment with chemopreventive agent was considered a toxic effect. The data were subjected to statistical analysis for the incidence to determine the effectiveness of the potential chemopreventive agents.
Figure IA shows a representative photograph of alveolar lesions in a DMBA treated gland and its comparison with a gland that was treated with DMBA along with a chemopreventive agent. The effects of p28 on the development of alveolar lesion are shown in Figures I B- IF and summarized in Figure 2. The peptide p28 inhibited MAL formation by 6?% at 25 μg/'ml concentration. Increasing concentration further up to 100 μg/ml did not enhance the efficacy of the peptide. The comparison of the peptide with azurin indicated that p28 was as effective as azurin for MAL development. Azurin at 50 μg/ml concentration resulted in a 67% inhibition. Statistical analyses indicated that the effect of p28 was statistically significant compared to DMBA control at concentrations greater than 12-5 μg ml fp<0.01 , Fisher's Exact Test; Chi Square analysis). Histopathological Evaluation of MDL. For MDL, the glands were processed for histopathological evaluations. The glands were sectioned longitudinally into 5-micron sections and stained with eosin hematoxeline. The longitudinal section of each gland was divided into several fields and each field was evaluated for ductal lesions. Mehta et a!.. 3. Natl. Cancer Inst. 93: 1 103-1106 (2001). Briefly, the entire gland is evaluated under the scope; smaller glands will have fewer total fields as compared to larger glands. Thus, each gland will have variable number of fields. Often the number of sections through the ducts also varies greatly from gland to gland. This results in the variable number from group to group. Fields containing ductal hyperplasia or atypia were determined and were compared with total number of field evaluated for each gland. No discrimination is made between the hyperplasia or atypia and severely occluded glands. Any field containing any of these histological patterns was considered positive for the lesion. The treatment groups were compared with the controls for the severity and percent inhibition was calculated.
Figure 3 shows a representative ductal lesion. DMBA induces ductal lesions varying from hyperplasia, atypia to complete occlusion of the ducts. A ratio of ductal lesions/total number of ductal sections was determined. Again, 12.5 μg/ml concentration of p28 suppressed only 15% of the MDL formation. However, at 25 μg/ml there was a significant inhibition of the lesions comparable to that observed with 50 μg/ml azurin. The efficacy of p28 at concentrations greater than 12.5 μg/ml was statistically significant (p<0.01, Fishers Exact Test). These results are summarized in Figure 4. Often effects of chemopreventive agents can be differentiated between the MAL and MDL. For example tamoxifen inhibited the development of MDL but not MAL, It is interesting to note that azurin and p28 inhibited both estrogen and progesterone-dependent ductal lesions as well as independent alveolar lesions. This example indicates that both p28 and azurin can pre\ cm the development of precancerous lesions m breast tissue. Thus, p28 and azunrt may be used as chemopreventive agents in mammalian patients.
Example 2. Selective Penetration of Cancer CeHs by Cupredoxins and Derivative Peptides as Potential vectors for Gene Delivery
We demonstrated that azuπn a member of the eupredoxin family of proteins, isolated from PscuJomonas aeruginosa enters cancer cells and induces a p53~mediated apoptosfs in vitro and in vivo. The selecthity of penetration of cationic and anionic cupredoxins and derived peptides as potential vectors for gene delivery was evaluated. The following cupredoxins were tested: azurin (14kDa. pi 5.7), rustieyanin (17kDa, pi 8.0), and plastocyanin (1 IkDa, pi 5.4), The results indicated that azurin had the most selective penetration.
25 amino acid (a. a.) fragments of azurin (azu) were synthesized and evaluated for their penetration into a variety of cancer and histological)' matched normal cells. Confocal microscopic and flow cytometric (FACS) analysis demonstrated that an 18 amino acid (1.7kDa, azu 50-67) fragment (pi 8) labeled with Alexaftuor 568 (800Da) selecthely penetrated human melanoma (MeI-2,7,29), breast (MCF-7), ovarian (SK-OV3). pancreatic (CAPAN-2), glioblastoma (LN-229), astrocytoma (CCF-STTGl), prostate (LN-CAP), and kidney (ACFfN-CRLl 611) cell lines, but not their respective controls. LDH release and hemolysis assays showed that pi 8 did not disrupt cancer cell membrane structure during penetration or produce hemolysis of human erthrocytes, suggesting that p 18 penetrates human cancer cells without disrupting membrane structure. Pretreatment of MeI-2 cells with specific inhibitors of cell internalization (cytochalasin D; inhibition of actin polymerization, taxol; inhibition of microtubule depolymerization, chlorpromazine; inhibition of clathrin- mediated endocytosis, sodium azide; metabolic inhibition, or staurosporine; cell cycle inhibition) had a negligible effect on the penetration of pϊ8. However, incubation of Mel-2 cells with nystatin (caveolae formation inhibitor) and brefeldin A (golgi apparatus disruptor) significantly inhibited the penetration of pi 8, suggesting that endocytic processes may, in part, be involved in the penetration of pl8. Imaging of pl8 labeled with an infrared dye (λeπl 800nm) in afhymic mice bearing xenografted melanoma tumors clearly demonstrated selective uptake in primary s.c. tumors and distant organ metastases without accumulating in normal organs and tissues. As such, the peptides of the present intention, including in one embodiment, pi 8 appear to have significant utilization as a non-viral vector for gene (or an\ DIs A'RNA fragment) therapy.
Example 3 - PIasmid constructions
Plasmids expressing fusion glutathione S-transferase (GST)-truncated wt-azurin (azu) derivatήes %ere constructed by a polymerase chain reaction using proofreading DNA polymerase Figure 5 shows a schematic representation of \aπous truncated wt-a/urin constructs For pGST-aru 36-12H (SEQ ID NO' 34), <ui amplified PCR fragment wax introduced into the BamHl and EcoRl sites of the commercial GST expression vector pGEXSX (Arnersham Bioseiences, Piscataway, NJ 08855). The fragment was amplified with pUC19-azu as a template and primers, 5'-CGGGATCC CCG GCA ACC TGC CGA AGA ACG TCA TGG GC-3"(SEQ ID NO: 35) and 5'-CGGAATTC GCA TCA CTT CAG GGT CAG GG-3' (SEQ ID NO: 36). where the additionally introduced BamHl and EcoRI sites are underlined respectively. Carboxyl-terminus truncation oiazu gene was cumulatively performed by introducing a stop codon using QuickChange site-direct mutagenesis kit (Stratagene. La Jolla, CA 92037).
For pGST-azu 36-50(SEQ ID NO: 37). pGST-azu 36-^7 (SEQ ID NO: 38) and pGST- azu 36-89 (SEQ ID NO: 39), stop codons were introduced into Ser51, Ser78. and Gly90, respectively. The plasmid carrying pGST-azu 36-128 was used as template DNA. Three sets of oligonuclotides for site-direct mutagenesis are shown as follows. For pGST-azu 36-50: 5'- GGC CAC AAC TGG GTA CTG TGA ACC GCC GCC GAC ATG CAG-3' (SEQ ID NO: 40), and 5'-CTG CAT GTC GGC GGC GGT TCA CAG TAC CCA GTT GTG GCC-3' (SEQ ID NO: 41). For pGST-azu 36-77: 5'-CCT GAA GCC CGA CGA CTG ACG TGT
CAT CGC CCA CAC C-3' (SEQ ID NO: 42) and 5'-GGT GTG GGC GAT GAC ACG TCA GTC GTC GGG CTT CAG G-3' (SEQ ID NO: 43). For pGST-azu 36-89: 5'-CCA AGC TGA TCG GCT CGT GAG AGAAGG ACT CGG TGA CC-3' (SEQ ID NO: 44), and 5'- GGT CAC CGA GTC CTT CTC TCA CGA GCC GAT CAG CTT GG-3 (SEQ ID NO: 45). The plasmids pGST-azu 50-77 and pGST-azu 67-77 were generated by PCR using pGST-azu 36-77 as a template DNA.
Amplified PCR fragments, azu 50-77 and azu 67-77, were obtained using forward primers 5'-CGGGATCC TGA GCA CCG CCG CCG ACA TGC AGG G-3' (SEQ ID NO: 46) and 5'-CGGGATCC CCG GCC TGG ACA AGG ATT ACC TGA AGC CCG-3 (SEQ ID NO: 47), where the additionally introduced BamHl site is indicated by underlining. The reverse primer, 5'-CGGAATTC GCA TCA CTT CAG GGT CAG GG-3' (SEQ ID NO: 48), was utilized in both cases.
The plasmid carrying gst-azu 50-7" was used for generating pGST-azu 50-66 by introduction of a stop codon in GIy67 using oligonuclotides as follows: 5'-GAC GGC ATG GCT TCC TGA CTG GAC AAG GAT TAC C -3" (SEQ ID NO: 49), and 5!-GGT AAT CCT TGT CCA GTC AGG AAG CCA TGC CGTC- 3' (SEQ ID NO: 50), The green fluorescent protein gene {gfp\ encoding the green fluorescent protein was also amplified by PCR. Forward and reverse primers used were 5'-CGGGATCC CCA TGG TGA GCA AGGGCG-3' (SEQ ID NO: 51) and 5'-CGGAATTC CTT GTA CAG CTC GTC CAT GCC G-3' (SEQ ID NO: 52) containing BamHl and EcoRl sites at the 55 end of each oligomiclotides. The resultant PCR fragment was ligated into the pGEXSX vector for creating pGST-GFP. For the preparation of plasmid DNA carrying gst-gfp-azu 50-77, the azu 50-77 geoe was amplified by PCR with pGST-a/u 50-77 as a template and primers 5' - CCGCTCGAG CCT GAG CAC CGC CGC CATGCA GGG-3' (SEQ ID NO: 53) and 5' - TTTTCCTTTTGCGGCCGC TCA GTC GTC GGG CTT CAG GTA ATC C-3" (SEQ ID NO: 54), where the introduced Xho I and .Vo/ 1 sites are underlined respectively. Purified azu 50-77 fragment was introduced into pGST-GFP at Xlio 1 and Not 1 unique restriction enzyme sites
Example 4 - Purification of Proteins
Wt-azurin and M44KM64E mutant azurin were prepared and purified as described by Yamada, T. et al. Proc. Natl. Acad, Sci. USA, vol. 1 OL pp. 4770-75 (2004), and in copending U.S. patent application serial number 10/720,603, the contents of which are incorporated by this reference. Briefly, the wt-azurin gene was amplified by PCR according to the method described by Kukimoto et ah, FEBS Lett, vol. 394, pp 87-90 (1996). PCR was performed using genomic DNA from P. aeruginosa strain PAOl as a template DNA. The amplified DNA fragment of 545 bp, digested with Hindlll and Ps tl, was inserted into the corresponding sites of pUC19 so that the azurin gene was placed downstream of the lac promoter to yield an expression plasmid pUC19-azuA. E. col JM 109 was used as a host strain for expression of the azurin gene. The recombinant E, coil strain was cultivated in 2YT medium containing 50 μg ml ampicillln, 0.1 mλl IPTG: and 0.5 mM CUSOΛ for 16 h at 37°C to produce azurin.
For preparation of the M44KM64E mutant azurin, site-directed mutagenesis of the azurin gene was performed using a QuickChange site-directed mutagenesis kit (Stratagene. La Jolla, CA). Mutations were confirmed by DNA sequencing.
Plasmid DNA, pET9a carrying the rus gene encoding the cupredoxin rusticyanin from Λcidithiohadϊlns ferrooxidans, was obtained from Dr. Kazuhiko Sasaki. Central Research institute of Electric Power Industrv, Cliiha, Japan. Rusticyanin was isolated from E. coli BL21 (DE3) harboring the nis gene using the method of Sasaki, K., et al. Biosci. Biotechnol. Biochem., vol. 67. pp. 1039-47 (2003) with some modifications. Briefly, acetic acid buffer (pH 4.0) and CM-Sepharose (Sigma Chemicals, St. Louis, MO 63178) were used instead of beta-alanin buffer (pH 4.0) and TSK- gel CM-650 column (Tosoh Bioscience, LLC, Montgomeryville, PA 18936). Two other purified cupredoxins, plastocyanin from Phormidium laminosum and pseudoazurin from Achromobacter cycloclastes were obtained from Dr. Beatrix G. Schlarb-Ridley, University of Cambridge, UK and Dr. Christopher Denmson, University of Newcastle Upon Tyne, UK, respectively. All recombinant GST-fusion derivatives were purified as follows: E. coli BL21 cells were used as the host strain. After induction with 0,4 mM IPTG at early log phase of growth in L broth, GST- fusion proteins were purified from cell extracts by using Glutathione Sepharose 4B affinity chromatography and Sephadex 75 gel- filtration column with PBS (Amersham Biosciences, Piscataway, NJ 08855). Purified proteins, wt azurin and GST- derivatives or other cupredoxins, labeled with ALEXA FLUOR* (Molecular Probes, Inc., Eugene, OR 97402) were isolated according to manufacturer's instructions. Unbound free fluorescent chemical was removed by gel-filtration column.
Example 5 - Cell cultures J774 and UISO-Mel-2 cells (available from Frederick Cancer Research and
Development Center, Frederick, Maryland U.S.A.) were cultured as described in Yamada, T. et at. Infect. Immun. vol. 70, pp. 7054-62 (2002); Goto, M., et al MoI. Microbiol, vol. 47, pp. 549-59 (2003); and Yamada, T., et al. Proc. Natl. Acad. Sci. USA vol. 99. pp. 14098-103 (2002), the contents of which are incorporated by reference. Human normal fibroblast cells (stock culture collection of the Department of Surgical Oncology, University of Illinois at Chicago (UIC), Chicago) were cultured in MEM with Eagle's salt containing 2 mM L- glutamine, 0.1 mM MEM essential amino acids and supplemented with 10% heat inactivated fetal bovine serum, 100 Units/ml penicillin and 100 μg/m! streptomycin. MCF- 7 and MGF- 1OF cells were cultured as described in Punj et al. Oncogene 23:2367-78 (2004). Example 6 - Co-culture of J774, UISO-Λlei-2 and Fibroblast Cells and Confocal microscopy
J774, UISO-Mel-2, and fibroblast cells were cultured on individual cover slips. After overnight incubation, the cells were washed with fresh media and all three cell lines were placed on a culture dish containing 200 μg'ml of wt-azurin conjugated with ALEXA1 FLUOR* 568. The cells were then incubated for 0.5 or 3.5 h at 370C under 5% CO2.
For preparation of microscope samples, cells were cultured on cover-slips overnight at 37yC. Cultured cells were placed at 37ύC or 40C for 2 h before protein treatment. Pre- warmed 37υC fresh media or ice-cold 4υC fresh media were mixed with red- fluorescent (labeled with ALEXA FLUOR^ 568) cupredoxins or GST- fusion derivatives, and incubated with the cells. The cells were washed with PBS, and fixed with methanol at -2O0C for 5 min. After washing with PBS twice and the addition of mounting media containing 1.5 μg/ml 4',6- diamidino-2-phenylindαle (DAPI) for staining nuclei (VECTASHILD, Vector, Burlingame. CA), images were taken by a confocal microscope.
Example 7 - Entry of Cupredoxins into J774 Cells Wt-azurin, its mutant variant M44KM64E, piastocyanin, pseudoazurin and rusticyanin were incubated with J774 cells as in Example 6 and the cells examined using confocal microscopy. In these experiments, the cupredoxins were conjugated with ALEXA FLUOR® 568 to fluoresce red and incubated with the J774 cells for 1 hr at 370C at a concentration of 200 μg/ml, and in a separate experiment wild type azurin and rusticyanin were incubated with J774 cells for 1 hr at 37°C at a concentration of about 6 to 7 μM. The nucleus was stained blue with DAPL A control without the proteins was maintained. In all cases, the cupredoxins were seen to enter into the cytosol of J774 cells. In similar experiments, auracyanin A and B enter preferentially to MCF7 cancer cells and not noncancerous control cells.
Example 8 - Entry of Wt-azurin and Rusticyanin into Various Cell Types
Wt-azurin exhibits a reduced cytotoxic activity towards MCF-IOF cells as contrasted with the MCF-7 cells. Punj ct al Oncogene 23:2367-2378 (2004). J774. peritoneal macrophages, mast cells, human breast cancer MCF-7 and human normal epithelial VfCF- I OF cells (stock culture collection of the Department of Surgical Oncology, University of Illinois at Chicago (UIC), Chicago) were treated and examined as in Example 5 and tested to determine if wt-azurin could enter such cells.
Wt-azuπn was internalized in J774 cells during 45 mm incubation. However, it was internalized very inefficiently in peritoneal macrophages or mast cells. Even after 6 hr incubation, such cells showed only limited entry. Similarly, while wt-azurin entered the breast cancer MCF-? cells efficiently, it showed an extremely reduced rate of entry in the normal mammary MCF-IOF cells.
Alexa fluor^-conjugated azurin entered efficiently in UISOMel-2 and MCF-7 cancer cells but not in the normal mammary MCF 10Al cells. Alexa fluor* -conjugated rusticyanin, however, not only entered the cytosol of UISO-Mel-2 and MCF-7 cancer cells, but also in the normal MCF 10Al cells. Unlike in the cancer cells where rusticyanin was evenly distributed in the cytosol, in MCFlOAl cells, much of the rusticyanin was sequestered in the perinuclear space surrounding the nucleus.
Example 9 - Wt azurin-mediated Cytotoxicity and Growth Inhibition
To further assess the specificity of entry of wt-azurin in various cells, we determined the entry of Alexa fluor- conjugated wt-azurin in J774, UISO-Mel-2 and normal fibroblast cells during incubation at 370C for 30 min and 3.5 hr. Wt-azurin was seen to enter rapidly in J774 and UISO-Mel-2 cells in 30 mm; very little wt-azurin was seen in the cytosol of fibroblasts during this period. After 3.5 hr of incubation, only small amounts of wt-azurin were found in the fibroblasts.
A 3(4,5 dimethyl thiazol-2-yl-2, 5 tetrazolium bromide)( MTT) assay was performed for the measurement of the cytotoxicity of wt-azurin as described by Yamada, T.. et al. Infect. Immun. 70:7054-62 (2002), Goto, M.. et al. MoL Microbiol 47:549-59 (2003), and in co- pending U.S. patent application serial number 10 720.603, filed November 24. 2003, the contents of which are incorporated by reference. Figure Ub) shows that significant wt- azuπn-mediated cytotoxicity was observed only with J7~4 and UISO-Mel-2 cells during 24 hr incubation.
M44KM64E mutant azuπn showed very little apoptosϊs -inducing activity in J774 cells but at 1 mg,ml concentration significantly inhibited (about 95%; cell cycle progression at the G? to S phase. Ceil progression was analyzed by flow cytometry, as described by Hiraoka. Y. et al .. Proc Nad Acad. Sc USA, 101 6427-32 (2004) and Yamada, T. ct al Proc Natl Acad. ScL USA 101:4770-75 (2004), the contents of which are incorporated by reference. Figure I (a) shows that when the fibroblasts were treated with 500 μg.ml or I mg ml of M44KM64E mutant azurin, the extent of inhibition of cell cycle progression was about 20%.
Example 10 - Microinjection of Wt-azurin into Fibroblast and MCF-IOF ceils Wt-azurin was microinjected into fibroblast and MCF-IOF cells as using the method described by Punj. V., et aL, Oncogene 23:2367-78 (2004). Cells were examined for induction of apoptosis, leading to nuclear DNA condensation and fragmentation. Significant nuclear DNA (labeled blue with DAPI) condensation and fragmentation were observed in microinjected single cells after 5 hr incubation with wt-azurin, but not during a 30 min. incubation with azurin.
Example 11 - Internalization of Wt-azurin Fusion Derivatives at 37°C A series of GST fusions of wt-azurin truncated at both the N- and the C-terminal were prepared and purified as in Example 1 (Figure 2(a) and 2(b)). Using ALEXA FLUOR* 568 conjugated wt-azurin, GST and GST-azu fusion derivatives, internalization in J774 cells at 370C during 1 hr incubation was examined using the method descπbed in Example 5. The nucleus was stained blue with DAPL While wt-azurin was internalized, GST remained at the periphery of the cells and was not internalized. GST-azu 36-128 and GST-azu 36-89 were internalized, as was GST-azu 36- 77. Further truncations, however, demonstrated that while GST-azu 50-77 was internalized, GST-azu 36-50 was highly inefficient and appeared to form clumps on the surface.
Example 12 - Internalization of Azurin Fusion Derivatives at 4eC
Internalization of wt-azuπn and the GST-azu fusion derivatives m J774 cells incubated at 4l'C was examined. At 4C*C. internalization of wt-azurm mside J774 cells during 1 hr incubation was severely impaired, Similar impairment was also seen with GST-azu 36- 128 and GST-azu 36-89. The shorter GST-azu 36-77, GST-azu 50-77, GST-azu 50-66 and GST-azu 67~77 demonstrated severe impairment of internalization at 40C. Example 13 - Energy- Dependent Internalization of the GST-GFP-azu 50-77 Fusion Protein in J774 and Melanoma UISO-MeI-2 Cells
GST was fused with GFP to make a GST-GFP fusion derivative. Additionally, azu 50-77 was fused to the GST-GFP (Mr 53 kDa) fusion protein (Figure 6(a)). The mobility of the purified GST, GST-GFP and GST-GFP-azu 5G-77 fusion derivatives was examined on SDS-PAGE (Figure 6(b)). Detection was by Coomassie Blue staining and Western blotting using anti-azurin antibody (Figure ό(c))
Flow cytometric determination of J774 cells treated with varying concentrations of GST-GFP showed that this protein does bind to J774 cells. Flow cytometric separation of J774 cells treated with increasing concentrations of GST-GFP-azu 50-77 fusion protein demonstrated significantly reduced fluorescence than GST-GFP alone (Figure 7), It is to be noted that internalization of GFP in mammalian cells is known to lead to loss of fluorescence. This reduction of fluorescence is also apparent when J774 cells are treated with 200 μg^'ml of GST-GFP-azu 50-77 fusion protein and incubated for increasing periods of time at 370C. To determine if there is any difference in the binding and internalization profile of
GST-GFP and GST-GFP-azu 50-77, both J774 and UISO-Mel-2 cells were incubated with GST-GFP and GST-GFP-azu 50-77 at 370C and at 4°C. The green fluorescence was localized using confocal microscopy. In J774 cells, GST-GFP fusion protein bound to the surface and was not internalized both at 370C and at 4°C. In contrast, GST-GFP-azu 50-77 was found to be internalized at 37°C, but not at 4°C. In LTSO-Mel-2 cells, the GST-GFP fusion protein was retained on the surface both at 370C and at 4°C. In contrast, similar to J774 cells, GST-GFP-azu 50-77 fusion protein was seen to be internalized at 370C but not at 40C.
Example 14 - Wt-azurin Entry into Mammalian CeJIs by a Ceil Membrane
Penetration and an Endocytic Mechanism
If wt-azurin entry is solely dependent on receptor-mediated endocytosis, it could be blocked by protonophore carbonyl cyanide m-chlorophrnylhydrazone (CCCP), a mitochondrial uncoupler of energy generation, or preincubalion with unlabeled azurin or other cupredoxins that block the receptors, J774 and UISO-MeI- 2 cells were incubated with the eupredoxins at 10 fold excess concentration for 2 hr at 43C, the cells washed thoroughly to remove the eupredoxins. and incubated with ALEXA FLUOR* 568-conjugated azurin for 1 hr at 37°C. There was as much internalized azurin as in cells not treated with the cupredoxins. The effects of cytochalasin D (available from Sigma- Aldrieh, St, Louis, Mo 63195), a known inhibitor of receptor-mediated endocytosis that disrupts the cellular microfilament network, and Brefeldin A (available from Sigma- Aldrich, St. Louis, Mo 63195), which is known to disrupt the Goigi apparatus and inhibit classical vesicle-mediated secretion, were also tested. CCCP at 20 pM concentration significantly reduced the uptake of azurin in UISOMeI-2 cells as did 0.25 to 0.5 pM cytoehalasin D. Brefeldin A, on the other hand, had no significant effect.
Example 15 - Entry of a GST-PEDIII-azu 50-77 Fusion Derivative into UISO-
MeI-2 Cells
A GST-fusion of Pseudomonas aeruginosa exotoxin A domain III (PEDlII) was constructed as described by Hwang, J. et ctl, Cell 48: 129-36 (1987); Reiter, Y. and Pastan. L, Trends BiotechnoL 16:513-20 (1998). This GST-PEDlII fusion derivative contained amino acids 381-613 of the exotoxin A. PEDIlI is known to harbor ADP-ribosyl transferase activity and inhibits cellular protein synthesis in eukaryotic cells by inhibiting eukaryotic elongation factor 2.
Using PCR as described for the GST-GFP-azu 50-77, the azu 50-77 sequence was introduced to the carboxyl end of the GST-PEDIII fusion protein (Figure 8(a)). These two fusion proteins (GSTPEDIII and GST-PEDIII-azu 50-77) were purified by glutathione- sepharose 4B column chromatography as 52 and 54 kDa proteins (Fig. 8(b}). UISO-Mel-2 and normal fibroblast (FBT) cells were then incubated for 24 h at 37°C with various concentrations of these proteins and the extent of cell death measured by MTT assay as described in Example 9. While GST-PEDΪII demonstrated only low cytotoxic.!} . the GST-PEDIII-azu 50-77 fusion protein had high cytotoxicity because of efficient entry to UISO-Mel-2 ceib (Figure 8(c)j. In contrast, the fusion proteins demonstrated a low level of cytotoxicity towards the fibroblast cells. Example 16 - Destabilization of the α-helix in wt-Azurin has no Substantial Effect on its Internalization in UISO-Mel-2 Cells
To examine if the α-helix plays a role in azurin entry, three helix-destabilizing proline residues were introduced in positions 54. 61 and 70 of wt-azurin (Figure 6) and examined the entry of the full length A54PT61 PK70P mutant azurin into UISO-Mel-2 cells. Single and double mutations in these positions were also constructed and tested for entry. The A54PT61PK70P mutant azurin was prepared by site-directed mutagenesis of the azurin gene using the QuickChange site-directed mutagenesis kit (Stratagene, La Jolla. CA).
The mutants were incubated at 200 μg/ml with UISO-Mel-2 cells for 1 hr at 37°C, after which the fluorescence was localized by confocal microscopy. In all cases, the ALEXA FLUOR* 568-conjugated mutant azurins entered UISO-Mel-2 cells. Similarly, when the GST-GFP-azu 50-77 fusion protein, as weli as its triple A54PT61PK70P azu mutant variant, were examined for entry in UISO-Mel-2 cells, no significant difference was observed.
Example 17 - Entry of a GST-PEDM-Rustkyamn Fusion Derivative into UISO-
Mel-2 Cells
A GST- fusion of Pseudomonas aeruginosa exotoxin A domain III (PEDIH) and was constructed as in Example 15. Using PCR as described for the GST-GFP-azu 50-77, full- length rusticyanin sequence was introduced to the carboxyl end of the GST-PEDIII fusion protein. The fusion protein was purified by glutathione-sepharose 4B column chromatography. UISO-Mel-2 and FBT cells were then incubated for 24 h at 37°C with various concentrations of the fusion protein and the extent of cell death measured by MTT assays as described in Example 7.
The GST-PEDIII- rusticyanin fusion protein exhibited high cytotoxicity against UISO-Mel-2 ceils (Figure 9). In contrast, the fusion protein demonstrated only a low level of cytotoxicity towards the FBT cells.

Claims

What is claimed is:
1. An isolated peptide that is a variant, derivative or structural equivalent of a cupredoxin; and that can inhibit the development of premalignant lesions in mammalian tissue.
2. The isolated peptide of claim 1, wherein the cupredoxin is selected from the group consisting of azurm. pseudoazurin, plastocyanin. rusticyanin. Laz, auracyanin, steliac>anin and cucumber basic protein..
3. The isolated peptide of claim 2, wherein the cupredoxin is azurin.
4. The isolated peptide of claim 1, wherein the cupredoxin is from an organism selected from the group consisting of Pseudomonas aeruginosa, Alcaligenes faccalis, Achromobacter xylosoxidan, Bordetella bronchiseptica, Methylomonas sp, . Neisseria meningitidis, Neisseria gonorrhea, Pseudomonas fluorescent;, Pseudomonas chlororaphis, Xylella fasiidiosa and Vibrio parahaemolyticus.
5. The isolated peptide of claim 4, that is from Pseudomonas aeruginosa.
6. The isolated peptide of claim 1, which is part of a peptide selected from the group consisting of SEQ ID NOS: 1 , 3-19.
7. The isolated peptide of claim 1, to which a sequence selected from the group consisting of SEQ ID NOS: I5 3-19 has at least 80% amino acid sequence identity.
8. The isolated peptide of claim 1, which is a truncation of the cupredoxin.
9. The isolated peptide of claim 8, wherein the peptide is more than about 10 residues and not more than about 100 residues.
10. The isolated peptide of claim 8, wherein the peptide comprises a sequence selected from the group consisting of Pseudomonas aeruginosa azurin residues 50-77, Pseudomonas aeruginosa azurin residues 50-67, Pseudomonas aeruginosa azurin residues 36-88. and SEQ ID NOS: 20-24.
1 1. The isolated peptide of claim 10, wherein the peptide consists of a sequence selected from the group consisting of Pseudomonas aeruginosa azurin residues 50-77, Pseudomonas aeruginosa azurin residues 50-67, Pseudomonas aeruginosa azurin residues 36-88 and SEQ ΪD NOS: 20-24.
32. The isolated peptide of claim 1 « wherein the peptide comprises equivalent residues of a cupredoxin as a region of P 'seudomonas aeruginosa azurin selected from the group consisting of residues 50-77. residues 50-67 and residues 36-88.
13. A pharmaceutical composition, comprising at least one cupredoxin or peptide of claim 1 in a pharmaceutically acceptable carrier.
14. The pharmaceutical composition of claim 13 which comprises at least two of the eupredoxins or peptides.
15. The composition of claim 13, wherein the pharmaceutical composition is formulated for intravenous administration.
16. The composition of claim 13, wherein the cupredoxin is from an organism selected from the group consisting of Ps eudomonas aeruginosa, Alcatigenes faecalis, Achromobactβr xylosoxidan, Bordetella bronchiseptica, Methylomonas sp., Neisseria meningitidis, Neisseria gonorrhea, Pseudomonas fluoresceins, Pseudomonas chlororaphis. Xylella fastidiosa and Vibrio parahaemolγticus,
17. The composition of claim 16, wherein the cupredoxin is from Pseudomonas aeruginosa.
18. The composition of claim 13, wherein the cupredoxin is selected from the group consisting of SEQ ID NOS: 1, 3-19.
19. A method to treat a mammalian patient, comprising administering to the patient a therapeutically effective amount of the composition of claim 13.
20. The method of claim 19, wherein the patient is human.
21. The method of claim 19. wherein the patient is at a higher risk to develop cancer than the general population.
22. The method of claim 21 , wherein the cancer is selected from melanoma, breast, pancreas, glioblastoma, astrocytoma, lung, colorectal, neck and head, bladder, prostate, skin, and cervical cancer.
23. The method of claim 2! , wherein the patient has at least one high risk feature.
24. The method of claim 19, wherein the patient has premalignant lesions.
25. The method of claim 19. wherein the patient has been cured of cancer or premalignant lesions.
26. The method of claim 19, wherein the pharmaceutical composition is administered by a mode selected from the group consisting of intravenous injection, intramuscular injection, subcutaneous injection, inhalation, topical administration, transdermal patch, suppository, vitreous injection and oral.
27. The method of claim 24, wherein the mode of administration is by intravenous injection.
28. The method of claim 21, wherein the pharmaceutical composition is coadministered with at least one other chemoprevenrive drug.
29. The method of claim 26, wherein the pharmaceutical composition is administered at about the same time as another chemopreventive drug.
30. A kit comprising the composition of claim 13 in a vial.
31. The kit of claim 30, wherein the kit is designed for intravenous administration.
32. A method to study the development of cancer comprising contacting the mammalian cells with a cupredoxin or peptide of claim 1 ; and measuring the development of premalignant and malignant cells,
33. The method of claim 32, wherein the cells are human cells.
34. The method of claim 32, wherein the cells are mammary gland cells.
35. The method of claim 32, wherein the cells are induced to develop cancer.
36. An expression vector, which encodes the peptide of claim 1.
37. An isolated peptide that is a variant, derivative or structural equivalent of a cupredoxin; wherein the isolated peptide is coupled to a cargo compound and can selectively enter mammalian cancer cells.
38. The isolated peptide of claim 37. wherein the cupredoxin is from an organism selected from the group consisting of Pseudomonas aeruginosa. Alcaligencs jaecalis, Achromobactcr xylosoxidan. Bordctella broπchiseptica. Methylomonas sp . Neisseria meningitidis, Neisseria gonorrhea, Pseudomonas fluoresceins, Pseudomonas chlororaphis . Xylella jastidiosa and Vibrio parahaemolyticus
39. The isolated peptide of claim 37. wherein the cupredoxin is azuriπ.
40. The isolated peptide of claim 39. wherein the azurin is from Pseudomonas aeruginosa
41. The isolated peptide of claim 37 comprising SEQ ID NC); 25.
42. The isolated peptide of claim 37 consisting of SEQ ID NO: 25.
43. The isolated peptide of claim 37, which is a truncation of the cupredoxin.
44. The isolated peptide of claim 37, wherein the peptide is more than about 10 residues and not more than about 100 residues.
45. The isolated peptide of claim 37, wherein the peptide comprises a sequence selected from the group consisting of Pseudomonas aeruginosa azurin residues 50-77 (SEQ ID NG: 2), Pseudomonas aeruginosa azurin residues 50-67 (SEQ ID NO: 25), Pseudomonas aeruginosa azurin residues 36-88 (SEQ ID NO: 26), and SEQ ID NOS: 20-24.
46. The composition of claim 3^ wherein the cargo compound is DNA or RKA.
47. The composition of claim 46 wherein said cargo compound is an anti sense molecule.
48. The composition of claim 37 wherein the cargo compound retards or kills mammalian cancer cells.
49. The composition of claim 48 wherein the cargo compound is a cytotoxic drug.
50. The composition of claim 37 wherein the cargo compound is selected from the group consisting of a protein, lipoprotein, polypeptide, peptide, polysaccharide, nucleic acid, dye, microparticle, nanoparticle, toxin and drug.
51. The composition of claim 37 wherein the cargo compound is selected from the group consisting of a protein and a polypeptide and wherein the peptide is linked to the cargo compound to form a fusion protein.
52. The composition of claim 37 wherein the cargo compound is a toxin.
53. The composition of claim 37 wherein the cargo compound is a detectable substance.
54. A pharmaceutical composition comprising the composition of claim 37 and a pharmaceutically acceptable carrier.
55. A method comprising contacting a cell υr cells with the composition of claim
J / .
56. The method of claim 55, wherein the cell or cells originate from a patient suffering from cancer, and further comprising reintroducing the cell or cells into the patient.
57. The method of claim 55, wherein the ceil is a cancer cell.
5%. The method of claim 57, wherein the cell is a cancer cell selected from the group consisting of osteosarcoma cell, lung carcinoma cell, colon carcinoma cell, lymphoma celL leukemia ceil, soft tissue sarcoma cell, breast carcinoma cell, carcinoma cell, bladder carcinoma cell, melanoma cell, brain tumor cell and prostate carcinoma cell.
59. A method of treating a patient with cancer, wherein the composition of claim 37 is administered to said patient in a therapeutically effective amount.
60. The method of claim 59, wherein the complex is administered in a manner selected from the group consisting of intravenously, topically, subcutaneously, intramuscularly, and into tumor.
61. The method of claim 59, wherein the complex is co-adrninistered with another cancer treatment.
62. A method for imaging cancer in a patient, wherein the composition of claim 53 is administered to said patient, and the location of the cargo compound is detected.
63. The method of claim 62, wherein the cargo compound is an X-ray contrast agent and the location of the cargo compound is detected by X-ray CT.
64. The method of claim 62, wherein the cargo compound is a magnetic resonance imaging contrast agent and the location of the cargo compound is detected by MRI.
65. The method of claim 62, wherein the cargo compound is an ultrasound contrast agent and the location of the cargo compound is detected by ultrasound imaging.
66. A method for diagnosing cancer, wherein a cell is contacted with the composition of claim 53 and the location of the cargo molecule is detected.
67. A kit comprising a reagent comprising the composition of claim 37.
68. The kit of claim 67, further comprising a reagent comprising a pharmaceutically-acceptable adjuvant or excipient.
69. The kit of claim 67, further comprising a vehicle for administration of the reagent.
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